The structure of human Pdcd4 bound to the 40S small ribosomal subunit
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 [ DOI: doi:10.1038/s41467-024-50672-8 Pubmed: 39117603 ]
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us17 (18 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Spermidine (145 Da, Ligand)
- Small ribosomal subunit protein us2 (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es30 (6 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- Programmed cell death protein 4 (51 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es6 (28 kDa, Protein from Homo sapiens)
- 18s rrna (555 kDa, RNA from Homo sapiens)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es25 (13 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)
- 40s ribosome bound to pdcd4 (1 MDa, Complex from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es7 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es24 (15 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es4, x isoform (29 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
Structure of a human 48S translation initiation complex with eIF4F and eIF4A
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8oz0
Q-score: 0.391
Brito Querido J, Sokabe M, Diaz-Lopez I, Gordiyenko Y, Fraser CS, Ramakrishnan V
Nat Struct Mol Biol (2024) 31 pp. 455-464 [ Pubmed: 38287194 DOI: doi:10.1038/s41594-023-01196-0 ]
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 3 (51 kDa, Protein from Homo sapiens)
- 18s rrna (555 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- Mrna (67 kDa, RNA from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 2 (38 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- Eukaryotic initiation factor 4a-i (46 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- Human 48s translation initiation complex (Complex from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 4 gamma 1 (155 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 5 (49 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 1 (36 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 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)
- Trnaimet (24 kDa, RNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
Structure of a human 48S translational initiation complex
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6zmw
Q-score: 0.293
Brito Querido J, Sokabe M, Kraatz S, Gordiyenko Y, Skehel JM, Fraser CS, Ramakrishnan V
Science (2020) 369 pp. 1220-1227 [ Pubmed: 32883864 DOI: doi:10.1126/science.aba4904 ]
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 3 (51 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 48s initiation complex (Complex)
- Eukaryotic translation initiation factor 3 subunit j (29 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 2 (38 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- Eukaryotic initiation factor 4a-i (46 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 48s initiation complex (Complex from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- Mrna (9 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 1 (36 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- Initiator met-trna-i (24 kDa, RNA from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1 (12 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 4 gamma 1 (145 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
Structure of a human 48S translational initiation complex - head
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6ybs
Q-score: 0.529
Brito Querido J, Sokabe M, Kraatz S, Gordiyenko Y, Skehel JM, Fraser CS, Ramakrishnan V
Science (2020) 369 pp. 1220-1227 [ DOI: doi:10.1126/science.aba4904 Pubmed: 32883864 ]
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 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)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 48s initiation complex (Complex from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 5it7
Q-score: 0.358
Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernandez IS
eLife (2016) 5 [ Pubmed: 27159451 DOI: doi:10.7554/eLife.13567 ]
- Eef2 (Complex from Saccharomyces cerevisiae P283)
- 60s acidic ribosomal protein p0 (21 kDa, Protein from Yeast)
- Ubiquitin-40s ribosomal protein s27a (7 kDa, Protein from Yeast)
- Klla0b01474p (14 kDa, Protein from Yeast)
- 40s ribosomal protein s27 (8 kDa, Protein from Yeast)
- 40s ribosomal protein s1 (24 kDa, Protein from Yeast)
- Klla0f18040p (16 kDa, Protein from Yeast)
- 5.8s ribosomal rna (50 kDa, RNA from Yeast)
- Magnesium ion (24 Da, Ligand)
- Klla0a07227p (20 kDa, Protein from Yeast)
- 60s ribosomal protein l39 (6 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s8 (22 kDa, Protein from Yeast)
- Ubiquitin fusion protein (5 kDa, Protein from Yeast)
- Klla0e23651p (17 kDa, Protein from Yeast)
- 40s ribosomal protein s29 (6 kDa, Protein from Yeast)
- 18s ribosomal rna (579 kDa, RNA from Yeast)
- Klla0b04686p (19 kDa, Protein from Yeast)
- Klla0c13519p (21 kDa, Protein from Yeast)
- Klla0d10659p (22 kDa, Protein from Yeast)
- Klla0b05742p (14 kDa, Protein from Yeast)
- Klla0f07843p (13 kDa, Protein from Yeast)
- Klla0e03455p (15 kDa, Protein from Yeast)
- Klla0e00573p (25 kDa, Protein from Yeast)
- Klla0a10483p (17 kDa, Protein from Yeast)
- Eft2p (91 kDa, Protein from Saccharomyces cerevisiae P283)
- Kluyveromyces lactis 80s ribosome in complex with the cricket paralysis virus ires and eef2 (4 MDa, Complex)
- 25s ribosomal rna (1 MDa, Macromolecule from Yeast)
- Klla0e05941p (9 kDa, Protein from Yeast)
- 60s ribosomal protein l3 (43 kDa, Protein from Yeast)
- 40s ribosomal protein s6 (25 kDa, Protein from Yeast)
- Klla0b13409p (14 kDa, Protein from Yeast)
- Rps23 (16 kDa, Protein from Yeast)
- Klla0c08371p (13 kDa, Protein from Yeast)
- 40s ribosomal protein s4 (29 kDa, Protein from Yeast)
- Klla0d05643p (24 kDa, Protein from Yeast)
- 5s ribosomal rna (38 kDa, RNA from Yeast)
- 60s ribosomal protein l44 (11 kDa, Protein from Yeast)
- 40s ribosomal protein s22 (14 kDa, Protein from Yeast)
- 60s ribosomal protein l20 (20 kDa, Protein from Yeast)
- Klla0c18216p (8 kDa, Protein from Yeast)
- 40s ribosomal protein s16 (15 kDa, Protein from Yeast)
- Klla0f04499p (21 kDa, Protein from Yeast)
- Kluyveromyces lactis 80s ribosome (Complex from Kluyveromyces lactis)
- Klla0f08261p (19 kDa, Protein from Yeast)
- 40s ribosomal protein s21 (9 kDa, Protein from Yeast)
- Klla0c04809p (6 kDa, Protein from Yeast)
- 60s ribosomal protein l13 (22 kDa, Protein from Yeast)
- 60s ribosomal protein l41-a (3 kDa, Protein from Baker's yeast)
- Klla0a07194p (15 kDa, Protein from Yeast)
- 60s ribosomal protein l36 (10 kDa, Protein from Yeast)
- Klla0d05181p (11 kDa, Protein from Yeast)
- Cricket paralysis virus ires (60 kDa, Macromolecule from Cricket paralysis virus)
- Klla0d08305p (24 kDa, Protein from Yeast)
- Klla0f05247p (13 kDa, Protein from Yeast)
- Klla0f25542p (12 kDa, Protein from Yeast)
- Klla0d07405p (11 kDa, Protein from Yeast)
- 40s ribosomal protein s0 (22 kDa, Protein from Yeast)
- Klla0b02937p (12 kDa, Protein from Yeast)
- (2s)-1-amino-n,n,n-trimethyl-1-oxobutan-2-aminium (145 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Rpl28 (16 kDa, Protein from Yeast)
- 40s ribosomal protein s24 (15 kDa, Protein from Yeast)
- Klla0e06997p (13 kDa, Protein from Yeast)
- Ul11 (12 kDa, Protein from Yeast)
- 60s ribosomal protein l25 (13 kDa, Protein from Yeast)
- Klla0d16071p (6 kDa, Protein from Yeast)
- 60s ribosomal protein l30 (10 kDa, Protein from Yeast)
- Klla0d03410p (25 kDa, Protein from Yeast)
- 40s ribosomal protein s12 (13 kDa, Protein from Yeast)
- 40s ribosomal protein s28 (7 kDa, Protein from Yeast)
- Ribosomal protein (24 kDa, Protein from Yeast)
- Cricket paralysis virus ires (Complex from Cricket paralysis virus)
- Klla0f04675p (22 kDa, Protein from Yeast)
- Klla0b01562p (16 kDa, Protein from Yeast)
- Klla0a06336p (20 kDa, Protein from Yeast)
- Ribosomal protein l15 (24 kDa, Protein from Yeast)
- Klla0e06843p (13 kDa, Protein from Yeast)
- Klla0e12277p (35 kDa, Protein from Yeast)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Klla0b06182p (7 kDa, Protein from Yeast)
- Klla0f09812p (23 kDa, Protein from Yeast)
- Klla0b08173p (11 kDa, Protein from Yeast)
- 40s ribosomal protein s14 (13 kDa, Protein from Yeast)
- Klla0b07139p (38 kDa, Protein from Yeast)
- Klla0e12453p (21 kDa, Protein from Yeast)
- Klla0d16027p (26 kDa, Protein from Yeast)
- Klla0d06941p (33 kDa, Protein from Yeast)
- Klla0d05115p (11 kDa, Protein from Yeast)
- 60s ribosomal protein l24 (7 kDa, Protein from Yeast)
- Klla0e23673p (20 kDa, Protein from Yeast)
- Ribosomal protein l37 (9 kDa, Protein from Yeast)