Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8skz
Q-score: 0.458
To Be Published
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (192-mer) (59 kDa, DNA from Homo sapiens)
- Dna (192-mer) (59 kDa, DNA from Homo sapiens)
- Cryo-em complex of ddm1-hells chimera bound to the nucleosome (Complex from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (12 kDa, Protein from Xenopus laevis)
- Atp-dependent dna helicase ddm1,lymphoid-specific helicase chimera (93 kDa, Protein from Arabidopsis thaliana)
- Adenosine-5'-diphosphate (427 Da, Ligand)
ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9dby
Q-score: 0.39
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9dde
Q-score: 0.456
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Histone h1.4 (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Ncprc1rybp bound to h2ak119ub/h1.4 chromatosome (Complex from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Histone h2a (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histones (Complex from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Dna (187-mer) (Complex from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 9dg3
Q-score: 0.382
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ncprc1rybp delta-linker mutant bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
ncPRC1RYBP bound to unmodified nucleosome
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 9dgg
Q-score: 0.47
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Ncprc1rybp bound to unmodified nucleosome (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9eoz
Q-score: 0.465
Ren M, Gut F, Fan Y, Ma J, Shan X, Yikilmazsoy A, Likhodeeva M, Hopfner KP, Zhou C
Nat Commun (2024) 15 pp. 9407-9407 [ Pubmed: 39477986 DOI: doi:10.1038/s41467-024-53811-3 ]
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Widom 601 dna (145-mer) (45 kDa, DNA from synthetic construct)
- Widom 601 dna (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Binary complex of human 8-oxoguanine glycosylase with nucleosome core particle (Complex)
- Widom 601 dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- N-glycosylase/dna lyase (40 kDa, Protein from Homo sapiens)
- Nucleosome core particle (Complex from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
Nucleosome containing 8oxoG at SHL-6
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vws
Q-score: 0.534
Cordero C, Mehta KPM, Weaver TM, Ling JA, Freudenthal BD, Cortez D, Roberts SA
Nat Commun (2024) 15 pp. 10722-10722 [ Pubmed: 39715760 DOI: doi:10.1038/s41467-024-55497-z ]
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 601 j strand (damaged strand) (45 kDa, DNA from synthetic construct)
- 601 i strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Nucleosome containing 8oxog at shl-6 (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8vwt
Q-score: 0.41
Cordero C, Mehta KPM, Weaver TM, Ling JA, Freudenthal BD, Cortez D, Roberts SA
Nat Commun (2024) 15 pp. 10722-10722 [ Pubmed: 39715760 DOI: doi:10.1038/s41467-024-55497-z ]
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 601 j strand (damaged strand) (45 kDa, DNA from synthetic construct)
- Ogg1 bound to a nucleosome containing 8oxog at shl-6 (composite map) (Complex from Homo sapiens)
- 601 i strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- N-glycosylase/dna lyase (38 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
Nucleosome containing 8oxoG at SHL4
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8vwu
Q-score: 0.559
Cordero C, Mehta KPM, Weaver TM, Ling JA, Freudenthal BD, Cortez D, Roberts SA
Nat Commun (2024) 15 pp. 10722-10722 [ DOI: doi:10.1038/s41467-024-55497-z Pubmed: 39715760 ]
- Nucleosome containing 8oxog at shl4 (Complex from Homo sapiens)
- 601 i strand (damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8vwv
Q-score: 0.359
Cordero C, Mehta KPM, Weaver TM, Ling JA, Freudenthal BD, Cortez D, Roberts SA
Nat Commun (2024) 15 pp. 10722-10722 [ DOI: doi:10.1038/s41467-024-55497-z Pubmed: 39715760 ]
- 601 i strand (damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Ogg1 bound to a nucleosome containing 8oxog at shl4 (composite map) (Complex from Homo sapiens)
- 601 j strand (non-damaged) (45 kDa, DNA from synthetic construct)
- N-glycosylase/dna lyase (38 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)