The structure of human Pdcd4 bound to the 40S-eIF4A-eIF3-eIF1 complex
Brito Querido J, Sokabe M, Diaz-Lopez I, Gordiyenko Y, Zuber P, Du Y, Albacete-Albacete L, Ramakrishnan V, Fraser CS
Nat Commun (2024) 15 pp. 6633-6633 [ Pubmed: 39117603 DOI: doi:10.1038/s41467-024-50672-8 ]
- Small ribosomal subunit protein es17 (15 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es26 (13 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us7 (22 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us19 (17 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es19 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us17 (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1 (12 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es8 (24 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (77 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es24 (15 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us2 (32 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es25 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es30 (6 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es7 (22 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es1 (30 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es12 (14 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Homo sapiens)
- Rrna (555 kDa, RNA from Homo sapiens)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Homo sapiens)
- Pdcd4-40s-eif4a-eif3-eif1 complex (2 MDa, Complex from Homo sapiens)
- Small ribosomal subunit protein us9 (16 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es21 (9 kDa, Protein from Homo sapiens)
- Eukaryotic initiation factor 4a-i (44 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es4, x isoform (29 kDa, Protein from Homo sapiens)
- Programmed cell death protein 4 (52 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- Spermidine (145 Da, Ligand)
- Small ribosomal subunit protein es32 (3 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us15 (17 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us13 (17 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us14 (6 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Acetic acid (60 Da, Ligand)
- Small ribosomal subunit protein es6 (28 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein us5 (31 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es27 (9 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es28 (7 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us10 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
Structure of human 48S translation initiation complex in open codon scanning state (48S-1)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8pj1
Q-score: 0.368
Petrychenko V, Yi SH, Liedtke D, Peng BZ, Rodnina MV, Fischer N
Nat Struct Mol Biol (2024) [ Pubmed: 39289545 DOI: doi:10.1038/s41594-024-01378-4 ]
- Mrna (82 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1 (12 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Human 48s initiation complex 40s-eif1-eif1a-eif2-eif3-trna-met-mrna (Complex from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- Methionine (149 Da, Ligand)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 2 (38 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 3 (51 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- Initiator met-trna-i (24 kDa, RNA from Homo sapiens)
- Ubiquitin (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 1 (36 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8pj2
Q-score: 0.32
Petrychenko V, Yi SH, Liedtke D, Peng BZ, Rodnina MV, Fischer N
Nat Struct Mol Biol (2024) [ Pubmed: 39289545 DOI: doi:10.1038/s41594-024-01378-4 ]
- Mrna (82 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- Human 48s initiation complex (Complex from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- Human 48s initiation complex 40s-eif1a-eif2-eif3-eif5-trna-met-mrna (Complex)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Mrna, 18s rrna, eukaryotic translation initiation factor 1a, x-chromosomal, initiator met-trna-i and eukaryotic translation initiation factor 5 (Complex from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 5 (49 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 3 (51 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- Initiator met-trna-i (24 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 1 (36 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8pj3
Q-score: 0.312
Petrychenko V, Yi SH, Liedtke D, Peng BZ, Rodnina MV, Fischer N
Nat Struct Mol Biol (2024) [ Pubmed: 39289545 DOI: doi:10.1038/s41594-024-01378-4 ]
- Mrna (82 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Human 48s initiation complex 40s-eif1a-eif2-eif3-eif5-eif5b-trna-met-mrna (Complex from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 5 (49 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 5b (139 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es30 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 3 (51 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- Initiator met-trna-i (24 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- Sodium ion (22 Da, Ligand)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 1 (36 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
Structure of human 48S translation initiation complex after eIF5 release (48S-4)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8pj4
Q-score: 0.361
Petrychenko V, Yi SH, Liedtke D, Peng BZ, Rodnina MV, Fischer N
Nat Struct Mol Biol (2025) 32 pp. 62-72 [ Pubmed: 39289545 DOI: doi:10.1038/s41594-024-01378-4 ]
- Mrna (82 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- Human 48s initiation complex 40s-eif1a-eif2-eif3-eif5b-trna-met-mrna (Complex from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 5b (139 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es30 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 3 (51 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- Initiator met-trna-i (24 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- Sodium ion (22 Da, Ligand)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 1 (36 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8pj5
Q-score: 0.437
Petrychenko V, Yi SH, Liedtke D, Peng BZ, Rodnina MV, Fischer N
Nat Struct Mol Biol (2024) [ Pubmed: 39289545 DOI: doi:10.1038/s41594-024-01378-4 ]
- Mrna (82 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 5b (139 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- Initiator met-trna-i (24 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Human 48s initiation complex 40s-eif1a-eif3-eif5-eif5b-trna-met-mrna (Complex from Homo sapiens)
- Ubiquitin (18 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8pj6
Q-score: 0.374
Petrychenko V, Yi SH, Liedtke D, Peng BZ, Rodnina MV, Fischer N
Nat Struct Mol Biol (2024) [ Pubmed: 39289545 DOI: doi:10.1038/s41594-024-01378-4 ]
- Mrna (82 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- Human 48s initiation complex 40s-eif1a-eif3-trna-met-mrna (Complex from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- Initiator met-trna-i (24 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
Structure of the human ATP synthase bound to bedaquiline (membrane domain)
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8khf
Q-score: 0.508
Zhang Y, Lai Y, Zhou S, Ran T, Zhang Y, Zhao Z, Feng Z, Yu L, Xu J, Shi K, Wang J, Pang Y, Li L, Chen H, Guddat LW, Gao Y, Liu F, Rao Z, Gong H
Nature (2024) 631 pp. 409-414 [ Pubmed: 38961288 DOI: doi:10.1038/s41586-024-07605-8 ]
- Atp synthase subunit f, mitochondrial (10 kDa, Protein from Homo sapiens)
- Human atp synthase (Complex from Homo sapiens)
- Atp synthase subunit g, mitochondrial (11 kDa, Protein from Homo sapiens)
- Atp synthase subunit delta, mitochondrial (15 kDa, Protein from Homo sapiens)
- Atp synthase subunit atp5mj, mitochondrial (6 kDa, Protein from Homo sapiens)
- Atp synthase subunit e, mitochondrial (7 kDa, Protein from Homo sapiens)
- Atp synthase subunit gamma, mitochondrial (30 kDa, Protein from Homo sapiens)
- Atp synthase subunit d, mitochondrial (18 kDa, Protein from Homo sapiens)
- Bedaquiline (555 Da, Ligand)
- Atp synthase f(0) complex subunit c1, mitochondrial (7 kDa, Protein from Homo sapiens)
- Atp synthase f(0) complex subunit b1, mitochondrial (24 kDa, Protein from Homo sapiens)
- Atp synthase subunit epsilon, mitochondrial (5 kDa, Protein from Homo sapiens)
- Atp synthase protein 8 (8 kDa, Protein from Homo sapiens)
- Atp synthase subunit a (24 kDa, Protein from Homo sapiens)
Structure of the human ATP synthase bound to bedaquiline (composite)
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8ki3
Q-score: 0.547
Zhang Y, Lai Y, Zhou S, Ran T, Zhang Y, Zhao Z, Feng Z, Yu L, Xu J, Shi K, Wang J, Pang Y, Li L, Chen H, Guddat LW, Gao Y, Liu F, Rao Z, Gong H
Nature (2024) 631 pp. 409-414 [ Pubmed: 38961288 DOI: doi:10.1038/s41586-024-07605-8 ]
- Atp synthase subunit f, mitochondrial (10 kDa, Protein from Homo sapiens)
- Human atp synthase (Complex from Homo sapiens)
- Atp synthase subunit g, mitochondrial (11 kDa, Protein from Homo sapiens)
- Atp synthase subunit gamma, mitochondrial (30 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp synthase subunit alpha, mitochondrial (55 kDa, Protein from Homo sapiens)
- Atp synthase subunit beta, mitochondrial (51 kDa, Protein from Homo sapiens)
- Atp synthase subunit d, mitochondrial (18 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Atp synthase subunit o, mitochondrial (20 kDa, Protein from Homo sapiens)
- Atp synthase subunit atp5mj, mitochondrial (6 kDa, Protein from Homo sapiens)
- Atpase inhibitor, mitochondrial (9 kDa, Protein from Homo sapiens)
- Bedaquiline (555 Da, Ligand)
- Atp synthase f(0) complex subunit c1, mitochondrial (7 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Atp synthase f(0) complex subunit b1, mitochondrial (24 kDa, Protein from Homo sapiens)
- Atp synthase subunit delta, mitochondrial (15 kDa, Protein from Homo sapiens)
- Atp synthase subunit e, mitochondrial (7 kDa, Protein from Homo sapiens)
- Atp synthase-coupling factor 6, mitochondrial (12 kDa, Protein from Homo sapiens)
- Atp synthase subunit epsilon, mitochondrial (5 kDa, Protein from Homo sapiens)
- Atp synthase protein 8 (8 kDa, Protein from Homo sapiens)
- Atp synthase subunit a (24 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human 43S ribosome with PDCD4
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8xxn
Q-score: 0.374
Ye X, Huang Z, Li Y, Wang M, Meng W, Miao M, Cheng J
Cell Res (2024) 34 pp. 522-525 [ Pubmed: 38641729 DOI: doi:10.1038/s41422-024-00962-z ]
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- Eukaryotic initiation factor 4a-i (46 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- Programmed cell death protein 4 (51 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1 (12 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- 18s rrna (602 kDa, RNA from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- 43s ribosome with pdcd4 (Complex from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)