Nucleosome containing a 1-nt gap at SHL-4.5
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9dwf
Q-score: 0.526
Ryan BJ, Weaver TM, Freudenthal BD
To Be Published
- 601 k strand (damaged strand 2) (8 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Nucleosome containing a 1-nt gap at shl-4.5 (Complex from Homo sapiens)
- 601 i strand (damaged strand 1) (35 kDa, DNA from synthetic construct)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 1, composite)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9dwg
Q-score: 0.364
Ryan BJ, Weaver TM, Freudenthal BD
To Be Published
- 601 k strand (damaged strand 2) (8 kDa, DNA from synthetic construct)
- Dna polymerase beta (38 kDa, Protein from Homo sapiens)
- Dna polymerase beta bound to a nucleosome containing a 1-nt gap at shl-4.5 (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- 601 i strand (damaged strand 1) (35 kDa, DNA from synthetic construct)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 2, composite)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9dwh
Q-score: 0.384
Ryan BJ, Weaver TM, Freudenthal BD
To Be Published
- 601 k strand (damaged strand 2) (8 kDa, DNA from synthetic construct)
- Dna polymerase beta (38 kDa, Protein from Homo sapiens)
- Dna polymerase beta bound to a nucleosome containing a 1-nt gap at shl-4.5 (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- 601 i strand (damaged strand 1) (35 kDa, DNA from synthetic construct)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 3, composite)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9dwi
Q-score: 0.405
Ryan BJ, Weaver TM, Freudenthal BD
To Be Published
- 601 k strand (damaged strand 2) (8 kDa, DNA from synthetic construct)
- Dna polymerase beta (38 kDa, Protein from Homo sapiens)
- Dna polymerase beta bound to a nucleosome containing a 1-nt gap at shl-4.5 (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- 601 i strand (damaged strand 1) (35 kDa, DNA from synthetic construct)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-3.5
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 9dwk
Q-score: 0.297
Weaver TM, Ryan BJ, Freudenthal BD
To Be Published
- Dna polymerase beta (38 kDa, Protein from Homo sapiens)
- 601 i strand (damaged strand 1) (32 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- 601 k strand (damaged strand 2) (12 kDa, DNA from synthetic construct)
- Dna polymerase beta bound to a nucleosome containing a 1-nt gap at shl-3.5 (Complex from Homo sapiens)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
Nucleosome containing a 1-nt gap at SHL-5.5
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 9dwl
Q-score: 0.366
Ryan BJ, Weaver TM, Freudenthal BD
To Be Published
- Nucleosome containing a 1-nt gap at shl-5.5 (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- 601 k strand (damaged strand 2) (5 kDa, DNA from synthetic construct)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- 601 i strand (damaged strand 1) (38 kDa, DNA from synthetic construct)
DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 9dwm
Q-score: 0.31
Ryan BJ, Weaver TM, Freudenthal BD
To Be Published
- Dna polymerase beta (38 kDa, Protein from Homo sapiens)
- Nucleosome containing a 1-nt gap at shl-5.5 (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- 601 k strand (damaged strand 2) (5 kDa, DNA from synthetic construct)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- 601 i strand (damaged strand 1) (38 kDa, DNA from synthetic construct)
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
- Atp-dependent dna helicase ddm1,lymphoid-specific helicase chimera (93 kDa, Protein from Arabidopsis thaliana)
- Histone h4 (12 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (192-mer) (59 kDa, DNA from Homo sapiens)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Cryo-em complex of ddm1-hells chimera bound to the nucleosome (Complex from Arabidopsis thaliana)
- Dna (192-mer) (59 kDa, DNA from Homo sapiens)
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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
Map with best defined NZF RYBP of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h4 (Complex from Xenopus laevis)
- Dna (156-mer) (Complex from synthetic construct)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Dna (153-mer) (Complex from synthetic construct)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Ncprc1-rybp (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histones (Complex from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)