CryoEM Structure of E. coli Transcription-Coupled Ribonucleotide Excision Repair (TC-RER) complex
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7uwe
Q-score: 0.413
Hao Z, Gowder M, Proshkin S, Bharati BK, Epshtein V, Svetlov V, Shamovsky I, Nudler E
Cell (2023) 186 pp. 2425- [ DOI: doi:10.1016/j.cell.2023.04.029 Pubmed: 37196657 ]
- Dna (29-mer) (8 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Ribonuclease hii (21 kDa, Protein from Escherichia coli)
- Elongation complex(ec)-rnaseh2 complex (Complex from Escherichia coli)
- Dna (29-mer) (8 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Rna (18-mer) (5 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7uwh
Q-score: 0.458
Hao Z, Gowder M, Proshkin S, Bharati BK, Epshtein V, Svetlov V, Shamovsky I, Nudler E
Cell (2023) 186 pp. 2425- [ DOI: doi:10.1016/j.cell.2023.04.029 Pubmed: 37196657 ]
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Elongation complex(ec)-rnaseh2 complex bound to ribonucleotide substrate (Complex from Escherichia coli)
- Ribonuclease hii (21 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Rna (18-mer) (5 kDa, RNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna/rna (59-mer) (18 kDa, Macromolecule from Escherichia coli)
- Dna (59-mer) (18 kDa, DNA from Escherichia coli)
Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 7u5c
Q-score: 0.33
Cai SW, Zinder JC, Svetlov V, Bush MW, Nudler E, Walz T, de Lange T
Nat Struct Mol Biol (2022) 29 pp. 813-819 [ Pubmed: 35578024 DOI: doi:10.1038/s41594-022-00766-y ]
- Dna polymerase alpha catalytic subunit (129 kDa, Protein from Homo sapiens)
- Dna primase large subunit (59 kDa, Protein from Homo sapiens)
- Cst complex subunit stn1 (42 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Human cst bound to dna polymerase alpha(pola1 delta n)-primase in a recruitment state (500 kDa, Complex)
- Dna primase small subunit (49 kDa, Protein from Homo sapiens)
- Canonical telomeric dna sequence (5 kDa, DNA from Homo sapiens)
- Dna polymerase alpha subunit b (66 kDa, Protein from Homo sapiens)
- Cst complex subunit ten1 (13 kDa, Protein from Homo sapiens)
- Cst complex subunit ctc1 (135 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of PRC2:EZH1-AEBP2-JARID2
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7kso
Q-score: 0.379
Grau D, Zhang Y, Lee CH, Valencia-Sanchez M, Zhang J, Wang M, Holder M, Svetlov V, Tan D, Nudler E, Reinberg D, Walz T, Armache KJ
Nat Commun (2021) 12 pp. 714-714 [ Pubmed: 33514705 DOI: doi:10.1038/s41467-020-20775-z ]
- Histone-lysine n-methyltransferase ezh1 (85 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Prc2:ezh1-aebp2-jarid2 (330 kDa, Complex from Homo sapiens)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Polycomb protein suz12 (83 kDa, Protein from Homo sapiens)
- Zinc finger protein aebp2 (33 kDa, Protein from Homo sapiens)
- Protein jumonji (138 kDa, Protein from Homo sapiens)
PRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7ksr
Q-score: 0.287
Grau D, Zhang Y, Lee CH, Valencia-Sanchez M, Zhang J, Wang M, Holder M, Svetlov V, Tan D, Nudler E, Reinberg D, Walz T, Armache KJ
Nat Commun (2021) 12 pp. 714-714 [ Pubmed: 33514705 DOI: doi:10.1038/s41467-020-20775-z ]
- Histone-lysine n-methyltransferase ezh1 (85 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Prc2:ezh1_a from a prc2:ezh1 dimer bound to a nucleosome (266 kDa, Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Polycomb protein suz12 (83 kDa, Protein from Homo sapiens)
PRC2:EZH1_B from a dimeric PRC2 bound to a nucleosome
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 7ktp
Q-score: 0.207
Grau D, Zhang Y, Lee CH, Valencia-Sanchez M, Zhang J, Wang M, Holder M, Svetlov V, Tan D, Nudler E, Reinberg D, Walz T, Armache KJ
Nat Commun (2021) 12 pp. 714-714 [ Pubmed: 33514705 DOI: doi:10.1038/s41467-020-20775-z ]
- Histone-lysine n-methyltransferase ezh1 (85 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Prc2:ezh1_a from a prc2:ezh1 dimer bound to a nucleosome (266 kDa, Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Polycomb protein suz12 (83 kDa, Protein from Homo sapiens)
CryoEM Structure of E. coli Rho-dependent Transcription Pre-termination Complex
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6xas
Q-score: 0.334
Hao Z, Epshtein V, Kim KH, Proshkin S, Svetlov V, Kamarthapu V, Bharati B, Mironov A, Walz T, Nudler E
Mol Cell (2021) 81 pp. 281- [ Pubmed: 33296676 DOI: doi:10.1016/j.molcel.2020.11.013 ]
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna (29-mer) (8 kDa, DNA from Escherichia coli (strain K12))
- Dna (29-mer) (8 kDa, DNA from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Transcription termination/antitermination protein nusa (54 kDa, Protein from Escherichia coli (strain K12))
- Transcription termination factor rho (47 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- E. coli rho-dependent transcription pre-termination complex (726 kDa, Complex from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Rna (60-mer) (19 kDa, RNA from Escherichia coli (strain K12))
CryoEM Structure of E. coli Rho-dependent Transcription Pre-termination Complex bound with NusG
Resolution: 7.7 Å
EM Method: Single-particle
Fitted PDBs: 6xav
Q-score: 0.103
Hao Z, Epshtein V, Kim KH, Proshkin S, Svetlov V, Kamarthapu V, Bharati B, Mironov A, Walz T, Nudler E
Mol Cell (2021) 81 pp. 281- [ Pubmed: 33296676 DOI: doi:10.1016/j.molcel.2020.11.013 ]
- Transcription termination factor rho (47 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dna (29-mer) (9 kDa, DNA from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna (29-mer) (8 kDa, DNA from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- E. coli rho-dependent transcription pre-termination complex (726 kDa, Complex from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Rna (18-mer) (5 kDa, RNA from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli K-12)
- Transcription termination/antitermination protein nusa (54 kDa, Protein from Escherichia coli K-12)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Escherichia coli K-12)
Cdc48-Npl4 complex in the presence of ATP-gamma-S
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6chs
Q-score: 0.286
Bodnar NO, Kim KH, Ji Z, Wales TE, Svetlov V, Nudler E, Engen JR, Walz T, Rapoport TA
Nat Struct Mol Biol (2018) 25 pp. 616-622 [ DOI: doi:10.1038/s41594-018-0085-x Pubmed: 29967539 ]
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Npl4 (73 kDa, Protein from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- Putative cell division control protein (90 kDa, Protein from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- Cdc48-npl4/ufd1 complex (Cellular component from Chaetomium thermophilum)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)