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 [ DOI: doi:10.1038/s41467-024-50672-8 Pubmed: 39117603 ]
- Eukaryotic translation initiation factor 3 subunit b (77 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- Pdcd4-40s-eif4a-eif3-eif1 complex (2 MDa, Complex from Homo sapiens)
- Small ribosomal subunit protein us17 (18 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es27 (9 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es19 (16 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es25 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es24 (15 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Small ribosomal subunit protein es21 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Small ribosomal subunit protein es12 (14 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es28 (7 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us14 (6 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- Rrna (555 kDa, RNA from Homo sapiens)
- Eukaryotic initiation factor 4a-i (44 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es4, x isoform (29 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
- Acetic acid (60 Da, Ligand)
- Small ribosomal subunit protein es17 (15 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es10 (18 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es30 (6 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es32 (3 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es8 (24 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es26 (13 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us2 (32 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es7 (22 kDa, Protein from Homo sapiens)
- Programmed cell death protein 4 (52 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us19 (17 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us7 (22 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us15 (17 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es1 (30 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us10 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us9 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1 (12 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us5 (31 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es6 (28 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us13 (17 kDa, Protein from Homo sapiens)
- Spermidine (145 Da, Ligand)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 9bct
Q-score: 0.554
You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH
Nature (2024) 635 pp. 229-236 [ DOI: doi:10.1038/s41586-024-07979-9 Pubmed: 39322680 ]
- Dna-directed rna polymerase subunit a" (43 kDa, Protein from Thermococcus kodakarensis)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit l (11 kDa, Protein from Thermococcus kodakarensis)
- Rna (13 kDa, RNA from synthetic construct)
- Ftta-dependent transcription termination complex (556 kDa, Complex from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit e (21 kDa, Protein from Thermococcus kodakarensis)
- Template strand dna (11 kDa, DNA from synthetic construct)
- Non-template strand dna (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit p (5 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit f (14 kDa, Protein from Thermococcus kodakarensis)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (8 kDa, Protein from Thermococcus kodakarensis)
- Transcription termination factor ftta (73 kDa, Protein from Thermococcus kodakarensis)
- Transcription elongation factor spt5 (16 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit d (29 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit b (127 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit h (9 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit n (7 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit a' (103 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit k (6 kDa, Protein from Thermococcus kodakarensis)
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 9bcu
Q-score: 0.613
You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH
Nature (2024) 635 pp. 229-236 [ DOI: doi:10.1038/s41586-024-07979-9 Pubmed: 39322680 ]
- Dna-directed rna polymerase subunit a" (43 kDa, Protein from Thermococcus kodakarensis)
- Rna (29-mer) (16 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit l (11 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit e (21 kDa, Protein from Thermococcus kodakarensis)
- Template strand dna (11 kDa, DNA from synthetic construct)
- Non-template strand dna (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit p (5 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit f (14 kDa, Protein from Thermococcus kodakarensis)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (8 kDa, Protein from Thermococcus kodakarensis)
- Transcription termination factor ftta (73 kDa, Protein from Thermococcus kodakarensis)
- Transcription elongation factor spt5 (16 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit d (29 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit b (127 kDa, Protein from Thermococcus kodakarensis)
- Ftta-dependent transcription termination complex containing 52 nt rna (556 kDa, Complex from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit h (9 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit n (7 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit a' (103 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit k (6 kDa, Protein from Thermococcus kodakarensis)
Intact V-ATPase State 2 and synaptophysin complex in mouse brain isolated synaptic vesicles
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 9bra
Q-score: 0.284
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ Pubmed: 38838737 DOI: doi:10.1038/s41586-024-07610-x ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- Synaptophysin (34 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- Mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
Intact V-ATPase State 3 and synaptophysin complex in mouse brain isolated synaptic vesicles
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 9brq
Q-score: 0.271
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ Pubmed: 38838737 DOI: doi:10.1038/s41586-024-07610-x ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- Synaptophysin (34 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- Mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
Intact V-ATPase State 3 in synaptophysin knock-out isolated synaptic vesicles
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 9brr
Q-score: 0.3
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ Pubmed: 38838737 DOI: doi:10.1038/s41586-024-07610-x ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
Intact V-ATPase State 2 in synaptophysin knock-out isolated synaptic vesicles
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 9brs
Q-score: 0.277
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ Pubmed: 38838737 DOI: doi:10.1038/s41586-024-07610-x ]
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
Intact V-ATPase State 1 and synaptophysin complex in mouse brain isolated synaptic vesicles
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 9brt
Q-score: 0.271
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ Pubmed: 38838737 DOI: doi:10.1038/s41586-024-07610-x ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- Synaptophysin (34 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- Mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
Intact V-ATPase State 1 in synaptophysin knock-out isolated synaptic vesicles
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 9bru
Q-score: 0.262
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ Pubmed: 38838737 DOI: doi:10.1038/s41586-024-07610-x ]
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
Structural insights into human co-transcriptional capping - structure 1
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8p4a
Q-score: 0.344
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464-2477.e5 [ Pubmed: 37369200 DOI: doi:10.1016/j.molcel.2023.06.002 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna (29-mer) (8 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*ap*ap*ap*ap*cp*cp*cp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (6 kDa, RNA from unidentified)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna (38-mer) (11 kDa, DNA from unidentified)