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)
- Human 48s translation initiation complex (Complex from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 1 (36 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 3 (51 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- Trnaimet (24 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- 18s rrna (555 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s16 (16 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 2 subunit 2 (38 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 5 (49 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 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)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 4 gamma 1 (155 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- Eukaryotic initiation factor 4a-i (46 kDa, Protein from Homo sapiens)
- Mrna (67 kDa, RNA from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
S-layer of archaeon Sulfolobus acidocaldarius by subtomogram averaging
Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8rbx
Q-score: 0.037
Fianu I, Ochmann M, Walshe JL, Dybkov O, Cruz JN, Urlaub H, Cramer P
Nature (2024) [ DOI: doi:10.1038/s41586-024-07269-4 Pubmed: 38570683 ]
- Negative elongation factor c/d (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Histone h2a type 1 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Integrator complex subunit 15 (50 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Nelf-b,negative elongation factor b,negative elongation factor b,negative elongation factor b,negative elongation factor b,negative elongation factor b (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii (Complex from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dss1 (3 kDa, Protein from Trichoplusia ni)
- Nucleosome (Complex from Homo sapiens)
- Unk-unk-unk-unk-unk-unk-unk-unk (698 Da, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Integrator complex subunit 13 (80 kDa, Protein from Homo sapiens)
- Integrator-pp2a complex and nelf (Complex from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Integrator complex subunit 14 (57 kDa, Protein from Homo sapiens)
- Unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk (1 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dsif (Complex from Trichoplusia ni)
- Pre-termination complex (1 MDa, Complex)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Template dna (56 kDa, DNA from synthetic construct)
- Integrator complex subunit 7 (107 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h3.3c (15 kDa, Protein from Homo sapiens)
- Rna and dna (Complex from Sus scrofa)
- Non-template dna (45 kDa, DNA from synthetic construct)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Integrator complex subunit 10 (82 kDa, Protein from Homo sapiens)
- Rna (5 kDa, RNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
Structure of Integrator-PP2A-SOSS-CTD post-termination complex
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8rbz
Q-score: 0.293
Fianu I, Ochmann M, Walshe JL, Dybkov O, Cruz JN, Urlaub H, Cramer P
Nature (2024) [ DOI: doi:10.1038/s41586-024-07269-4 Pubmed: 38570683 ]
- Rna polymerase ii c-terminal domain peptides (Complex from Sus scrofa)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 15 (50 kDa, Protein from Homo sapiens)
- Integrator-pp2a complex and nabp2 and inip (Complex from Homo sapiens)
- Integrator complex subunit 13 (80 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Integrator complex subunit 14 (57 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Soss complex subunit b1 (22 kDa, Protein from Homo sapiens)
- Soss complex subunit c (11 kDa, Protein from Homo sapiens)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Unk-unk-unk-unk-unk-unk-unk-unk-unk (783 Da, Protein from Sus scrofa)
- Integrator complex subunit 3 (118 kDa, Protein from Homo sapiens)
- Dss1 (Complex from Trichoplusia ni)
- Integrator complex subunit 7 (107 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (1 kDa, Protein from Sus scrofa)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Integrator complex subunit 10 (82 kDa, Protein from Homo sapiens)
- Post-termination complex (1 MDa, Complex)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Dss1 (3 kDa, Protein from Trichoplusia ni)
Structure of Integrator-PP2A complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8rc4
Q-score: 0.036
Fianu I, Ochmann M, Walshe JL, Dybkov O, Cruz JN, Urlaub H, Cramer P
Nature (2024) [ DOI: doi:10.1038/s41586-024-07269-4 Pubmed: 38570683 ]
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 15 (50 kDa, Protein from Homo sapiens)
- Integrator-pp2a complex (1 MDa, Complex)
- Integrator complex subunit 13 (80 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Integrator complex subunit 14 (57 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Dss1 (Complex from Trichoplusia ni)
- Dss1 (3 kDa, Protein from Trichoplusia ni)
- Integrator complex subunit 7 (107 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Integrator-pp2a complex (Complex from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Integrator complex subunit 6 (101 kDa, Protein from Homo sapiens)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Integrator complex subunit 10 (82 kDa, Protein from Homo sapiens)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 8i7v
Q-score: 0.495
Park JH, Kawakami K, Ishimoto N, Ikuta T, Ohki M, Ekimoto T, Ikeguchi M, Lee DS, Lee YH, Tame JRH, Inoue A, Park SY
Nat Commun (2023) 14 pp. 7150-7150 [ DOI: doi:10.1038/s41467-023-42764-8 Pubmed: 37932263 ]
- 5-methyl-4-oxidanyl-pyrazin-4-ium-2-carboxylic acid (155 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (8 kDa, Protein from Homo sapiens)
- Acipomox bound human hydroxy-carboxylic acid receptor 2 in complex with gi heterotrimer (150 kDa, Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Human hydroxycarboxylic acid receptor 2,hydroxycarboxylic acid receptor 2,hydroxycarboxylic acid receptor 2 (54 kDa, Protein from Homo sapiens)
- Scfv16 (27 kDa, Protein from Mus musculus)
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8i7w
Q-score: 0.433
Park JH, Kawakami K, Ishimoto N, Ikuta T, Ohki M, Ekimoto T, Ikeguchi M, Lee DS, Lee YH, Tame JRH, Inoue A, Park SY
Nat Commun (2023) 14 pp. 7150-7150 [ DOI: doi:10.1038/s41467-023-42764-8 Pubmed: 37932263 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (8 kDa, Protein from Homo sapiens)
- Human hydroxycarboxylic acid receptor 2,hydroxycarboxylic acid receptor 2 (54 kDa, Protein from Homo sapiens)
- 8-chloranyl-3-pentyl-7h-purine-2,6-dione (256 Da, Ligand)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Gsk256073 bound human hydroxy-carboxylic acid receptor 2 in complex with gi heterotrimer (150 kDa, Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Scfv16 (27 kDa, Protein from Mus musculus)
Gi bound CCR8 complex with nonpeptide agonist LMD-009
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 8kfx
Q-score: 0.496
Jiang S, Lin X, Wu L, Wang L, Wu Y, Xu Z, Xu F
Sci Adv (2024) 10 pp. eadj7500-eadj7500 [ Pubmed: 38306437 DOI: doi:10.1126/sciadv.adj7500 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- C-c chemokine receptor type 8,fusion protein (65 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Gpcr gi complex with agonist (Complex from Homo sapiens)
- Scfv16 (31 kDa, Protein from Homo sapiens)
- 8-[[3-(2-methoxyphenoxy)phenyl]methyl]-1-(2-phenylethyl)-1,3,8-triazaspiro[4.5]decan-4-one (471 Da, Ligand)
Gi bound CCR8 complex with nonpeptide agonist ZK 756326
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8kfy
Q-score: 0.466
Jiang S, Lin X, Wu L, Wang L, Wu Y, Xu Z, Xu F
Sci Adv (2024) 10 pp. eadj7500-eadj7500 [ DOI: doi:10.1126/sciadv.adj7500 Pubmed: 38306437 ]
- Hetero complex (Complex from Homo sapiens)
- Scfv16 (31 kDa, Protein from Homo sapiens)
- 2-[2-[4-[(3-phenoxyphenyl)methyl]piperazin-1-yl]ethoxy]ethanol (356 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- C-c chemokine receptor type 8,fusion protein (65 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
Gi bound CCR8 in ligand free state
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8kfz
Q-score: 0.351
Jiang S, Lin X, Wu L, Wang L, Wu Y, Xu Z, Xu F
Sci Adv (2024) 10 pp. eadj7500-eadj7500 [ Pubmed: 38306437 DOI: doi:10.1126/sciadv.adj7500 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Hetero complex (Complex from Homo sapiens)
- C-c chemokine receptor type 8,lgbit fusion protein,recombinant human rhinovirus (65 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Scfv16 (31 kDa, Protein from Homo sapiens)