Damaged 70S ribosome with PrfH bound
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 9mor
Q-score: 0.367
Tian Y, Li Q, Fatma S, Jiang J, Jin H, Zeng F, Huang RH
bioRxiv (2025) [ Pubmed: 39829893 DOI: doi:10.1101/2025.01.09.632186 ]
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- Trna (Cellular component)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 50s (Complex)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli)
- Damaged 70s with prfh (Complex from Escherichia coli)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- 30s (Complex)
- Water (18 Da, Ligand)
- P-trna, e-trna (24 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- Mrna (8 kDa, RNA from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- Peptide chain release factor h (26 kDa, Protein from Capnocytophaga gingivalis)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli)
- Putative peptide chain release factor homolog (Cellular component)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
- 16s ribosomal rna (497 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
Damaged 70S ribosome with PrfH bound
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 9mq4
Q-score: 0.462
Tian Y, Li Q, Fatma S, Jiang J, Jin H, Zeng F, Huang RH
bioRxiv (2025) [ Pubmed: 39829893 DOI: doi:10.1101/2025.01.09.632186 ]
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- Trna (Cellular component)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 50s (Complex)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli)
- Damaged 70s with prfh (Complex from Escherichia coli)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- 30s (Complex)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli 0.1197)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- P-trna, e-trna (24 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- Mrna (8 kDa, RNA from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 16s ribosomal rna (497 kDa, RNA from Escherichia coli)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli)
- Putative peptide chain release factor homolog (Cellular component)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
- Peptide chain release factor h (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
Drosophila mojavensis gustatory receptor 43a(Gr43a) in Fructose-bound state
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 8ze3
Q-score: 0.509
Chen R, Zhang R, Li L, Wang B, Gao Z, Liu F, Chen Y, Tian Y, Li B, Chen Q
Cell Discov (2024) 10 pp. 83-83 [ Pubmed: 39103325 DOI: doi:10.1038/s41421-024-00716-6 ]
- Gustatory receptor (50 kDa, Protein from Drosophila mojavensis)
- Tetrameric fructose-specific receptor 43a of drosophila mojavensis (dmgr43a) (47 kDa, Complex from Drosophila mojavensis)
- Beta-d-fructofuranose (180 Da, Ligand)
Aplysia californica FaNaC in ligand bound state
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7yvb
Q-score: 0.539
Liu F, Dang Y, Li L, Feng H, Li J, Wang H, Zhang X, Zhang Z, Ye S, Tian Y, Chen Q
Nat Chem Biol (2023) 19 pp. 1276-1285 [ DOI: doi:10.1038/s41589-023-01401-7 Pubmed: 37550431 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fmrfamide-gated na+ channel (76 kDa, Protein from Aplysia californica)
- Trimeric fmrfamide activated sodium channel from aplysia californica (acfanac) (73 kDa, Complex from Aplysia californica)
- Phe-met-arg-phe-amide (599 Da, Protein from synthetic construct)
Aplysia californica FaNaC in apo state
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7yvc
Q-score: 0.532
Liu F, Dang Y, Li L, Feng H, Li J, Wang H, Zhang X, Zhang Z, Ye S, Tian Y, Chen Q
Nat Chem Biol (2023) 19 pp. 1276-1285 [ DOI: doi:10.1038/s41589-023-01401-7 Pubmed: 37550431 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fmrfamide-gated na+ channel (76 kDa, Protein from Aplysia californica)
- Trimeric fmrfamide activated sodium channel from aplysia californica (acfanac) (73 kDa, Complex from Aplysia californica)
- Calcium ion (40 Da, Ligand)
Damaged 70S ribosome with PrfH bound
Resolution: 2.55 Å
EM Method: Single-particle
Fitted PDBs: 7sa4
Q-score: 0.61
Tian Y, Zeng F, Raybarman A, Fatma S, Carruthers A, Li Q, Huang RH
PNAS (2022) 119 pp. e2202464119-e2202464119 [ DOI: doi:10.1073/pnas.2202464119 Pubmed: 35858322 ]
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- Trna (Cellular component)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- 50s (Complex)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- Damaged 70s with prfh (Complex from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- 30s (Complex)
- P-trna, e-trna (24 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- Mrna (8 kDa, RNA from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- Peptide chain release factor h (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Putative peptide chain release factor homolog (Cellular component)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
- 16s ribosomal rna (497 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
Structure of nucleosome-bound human BAF complex
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6ltj
Q-score: 0.007
He S, Wu Z, Tian Y, Yu Z, Yu J, Wang X, Li J, Liu B, Xu Y
Science (2020) 367 pp. 875-881 [ DOI: doi:10.1126/science.aaz9761 Pubmed: 32001526 ]
- Structure of nucleosome-bound human baf complex (Complex)
- Nucleosome (Complex from Xenopus calcaratus)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily d member 1 (58 kDa, Protein from Homo sapiens)
- Baf (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (119-mer) (36 kDa, DNA from Homo sapiens)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e member 1 (46 kDa, Protein from Homo sapiens)
- Dna (119-mer) (36 kDa, DNA from Homo sapiens)
- Actin, cytoplasmic 1 (41 kDa, Protein from Homo sapiens)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- At-rich interactive domain-containing protein 1a (142 kDa, Protein from Homo sapiens)
- Transcription activator brg1 (184 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.3 (15 kDa, Protein from Xenopus laevis)
- Swi/snf complex subunit smarcc2 (133 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (45 kDa, Protein from Homo sapiens)
- Zinc finger protein ubi-d4 (32 kDa, Protein from Homo sapiens)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily b member 1 (38 kDa, Protein from Homo sapiens)
Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state
Resolution: 4.31 Å
EM Method: Single-particle
Fitted PDBs: 5z3u
Q-score: 0.372
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z
Nature (2019) 567 pp. 409-413 [ DOI: doi:10.1038/s41586-019-1029-2 Pubmed: 30867599 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Complex of snf2 and nucleosome in adp befx state (300 kDa, Complex from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Transcription regulatory protein snf2 (85 kDa, Protein from Saccharomyces cerevisiae)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state
Resolution: 4.22 Å
EM Method: Single-particle
Fitted PDBs: 5z3v
Q-score: 0.356
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z
Nature (2019) 567 pp. 409-413 [ DOI: doi:10.1038/s41586-019-1029-2 Pubmed: 30867599 ]
- Transcription regulatory protein snf2 (85 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Complex of snf2 and nucleosome in adp befx state (300 kDa, Complex from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Structure of Snf2-nucleosome complex in ADP state
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 5z3o
Q-score: 0.349
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z
Nature (2019) 567 pp. 409-413 [ DOI: doi:10.1038/s41586-019-1029-2 Pubmed: 30867599 ]
- Transcription regulatory protein snf2 (85 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Complex of snf2 and nucleosome in adp state (300 kDa, Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)