BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8svf
Q-score: 0.383
Thomas JF, Valencia-Sanchez MI, Tamburri S, Gloor SL, Rustichelli S, Godinez-Lopez V, De Ioannes P, Lee R, Abini-Agbomson S, Gretarsson K, Burg JM, Hickman AR, Sun L, Gopinath S, Taylor HF, Sun ZW, Ezell RJ, Vaidya A, Meiners MJ, Cheek MA, Rice WJ, Svetlov V, Nudler E, Lu C, Keogh MC, Pasini D, Armache KJ
Sci Adv (2023) 9 pp. eadg9832-eadg9832 [ DOI: doi:10.1126/sciadv.adg9832 Pubmed: 37556531 ]
- Bap1/asxl1 bound to the h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ubiquitin carboxyl-terminal hydrolase bap1 (80 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna/rna (187-mer) (58 kDa, Macromolecule from synthetic construct)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Polycomb group protein asxl1 (165 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna/rna (327-mer) (102 kDa, Macromolecule from synthetic construct)
Map focused on acidic patch BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
Thomas JF, Valencia-Sanchez MI, Tamburri S, Gloor SL, Rustichelli S, Godinez-Lopez V, De Ioannes P, Lee R, Abini-Agbomson S, Gretarsson K, Burg JM, Hickman AR, Sun L, Gopinath S, Taylor HF, Sun ZW, Ezell RJ, Vaidya A, Meiners MJ, Cheek MA, Rice WJ, Svetlov V, Nudler E, Lu C, Keogh MC, Pasini D, Armache KJ
Sci Adv (2023) 9 pp. eadg9832-eadg9832 [ DOI: doi:10.1126/sciadv.adg9832 Pubmed: 37556531 ]
Overall map of BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
Thomas JF, Valencia-Sanchez MI, Tamburri S, Gloor SL, Rustichelli S, Godinez-Lopez V, De Ioannes P, Lee R, Abini-Agbomson S, Gretarsson K, Burg JM, Hickman AR, Sun L, Gopinath S, Taylor HF, Sun ZW, Ezell RJ, Vaidya A, Meiners MJ, Cheek MA, Rice WJ, Svetlov V, Nudler E, Lu C, Keogh MC, Pasini D, Armache KJ
Sci Adv (2023) 9 pp. eadg9832-eadg9832 [ DOI: doi:10.1126/sciadv.adg9832 Pubmed: 37556531 ]
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)
Human CST bound to full-length DNA polymerase alpha-primase in a recruitment state
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 ]
- Cst complex subunit ten1 (Protein from Homo sapiens)
- Telomeric g-strand ssdna (3 repeats) (DNA from Homo sapiens)
- Cst complex subunit ctc1 (Protein from Homo sapiens)
- Dna polymerase alpha catalytic subunit pola1 (Protein from Homo sapiens)
- Cst complex subunit stn1 (Protein from Homo sapiens)
- Dna primase large subunit prim2 (Protein from Homo sapiens)
- Dna primase catalytic subunit (Protein from Homo sapiens)
- Cst bound to full-length dna polymerase alpha-primase and ssdna (540 kDa, Complex)
- Dna polymerase alpha b subunit pola2 (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)
Nucleosome from a dimeric PRC2 bound to a nucleosome
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7ktq
Q-score: 0.494
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 h4 (8 kDa, Protein from Xenopus laevis)
- Histone h3 (11 kDa, Protein from Xenopus laevis)
- 601 dna (167-mer) (51 kDa, DNA from Homo sapiens)
- 601 dna (167-mer) (51 kDa, DNA from Homo sapiens)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- Nucleosome from a prc2:ezh1 dimer bound to a nucleosome (220 kDa, Complex from Xenopus laevis)
PRC2:EZH1 dimer bound to a nucleosome (composite map)
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 ]
- Aebp2 (Protein from Homo sapiens)
- Histone h2b (Protein from Xenopus laevis)
- Histone h2a (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- Ezh1 (Protein from Homo sapiens)
- Rbap48 (Protein from Homo sapiens)
- Histone h3 (Protein from Xenopus laevis)
- Eed (Protein from Homo sapiens)
- Prc2:ezh1_a from a prc2:ezh1 dimer bound to a nucleosome (266 kDa, Complex from Homo sapiens)
- Suz12 (Protein from Homo sapiens)
- Jarid2 (Protein from Homo sapiens)
- 167bp dna 601 strand (DNA 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))