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 h4 (Complex from Xenopus laevis)
- Histone h1.4 (Complex from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h2a (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Ncprc1rybp bound to h2ak119ub/h1.4 chromatosome (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Dna (187-mer) (Complex from synthetic construct)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ncprc1-rybp (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8v4y
Q-score: 0.53
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ Pubmed: 38472177 DOI: doi:10.1038/s41467-024-46178-y ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (forward strand) (63 kDa, DNA from synthetic construct)
- Beryllium trifluoride ion (66 Da, Ligand)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (300 kDa, Complex)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (reverse strand) (64 kDa, DNA from synthetic construct)
- Nucleosome with xenopus laevis histones (200 kDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (122 kDa, Protein from Homo sapiens)
- Snf2h (100 kDa, Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Cryo-EM structure of doubly-bound SNF2h-nucleosome complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8v6v
Q-score: 0.477
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ Pubmed: 38472177 DOI: doi:10.1038/s41467-024-46178-y ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (forward strand) (63 kDa, DNA from synthetic construct)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (300 kDa, Complex)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (reverse strand) (64 kDa, DNA from synthetic construct)
- Nucleosome with xenopus laevis histones (200 kDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (122 kDa, Protein from Homo sapiens)
- Snf2h (100 kDa, Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8v7l
Q-score: 0.456
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ Pubmed: 38472177 DOI: doi:10.1038/s41467-024-46178-y ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) plus 60 base pairs flanking dna (reverse strand) (64 kDa, DNA from synthetic construct)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (forward strand) (63 kDa, DNA from synthetic construct)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (300 kDa, Complex)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Nucleosome with xenopus laevis histones (200 kDa, Complex)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (122 kDa, Protein from Homo sapiens)
- Snf2h (100 kDa, Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Resolution: 5.7 Å
EM Method: Single-particle
Fitted PDBs: 8jh2
Q-score: 0.145
Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H
J Biol Chem (2023) 299 pp. 105477-105477 [ DOI: doi:10.1016/j.jbc.2023.105477 Pubmed: 37981206 ]
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*cp*cp*up*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*up*g)-3') (5 kDa, RNA from synthetic construct)
- Rna (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc27 (24 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii (Complex from Homo sapiens)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Histones (Complex from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Dna (Complex from synthetic construct)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8jh3
Q-score: 0.255
Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H
J Biol Chem (2023) 299 pp. 105477-105477 [ DOI: doi:10.1016/j.jbc.2023.105477 Pubmed: 37981206 ]
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*up*gp)-3') (4 kDa, RNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histones (Complex from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Dna (Complex from synthetic construct)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8jh4
Q-score: 0.313
Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H
J Biol Chem (2023) 299 pp. 105477-105477 [ DOI: doi:10.1016/j.jbc.2023.105477 Pubmed: 37981206 ]
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- Rna (5'-r(p*gp*up*cp*up*up*gp*gp*gp*up*gp)-3') (3 kDa, RNA from synthetic construct)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histones (Complex from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Dna (Complex from synthetic construct)
CryoEM Structure INO80core Hexasome complex composite map state1
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8oo7
Q-score: 0.556
Zhang M, Jungblut A, Kunert F, Hauptmann L, Hoffmann T, Kolesnikova O, Metzner F, Moldt M, Weis F, DiMaio F, Hopfner KP, Eustermann S
Science (2023) 381 pp. 313-319 [ Pubmed: 37384673 DOI: doi:10.1126/science.adf6287 ]
- Actin-related protein 5 (87 kDa, Protein from Thermochaetoides thermophila)
- Ino80 core module in complex with hexasome (861 kDa, Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Chromatin-remodeling complex subunit ies6 (23 kDa, Protein from Thermochaetoides thermophila)
- Histones (Complex from Homo sapiens)
- Dna strand 1 (69 kDa, DNA from synthetic construct)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Ruvb-like protein 2 (53 kDa, Protein from Thermochaetoides thermophila)
- Histone h2a (14 kDa, Protein from Homo sapiens)
- Chromatin remodeler ino80 (Complex from Thermochaetoides thermophila)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Ruvb-like protein 1 (50 kDa, Protein from Thermochaetoides thermophila)
- Ino eighty subunit 2 (53 kDa, Protein from Thermochaetoides thermophila)
- Chromatin-remodeling atpase ino80 (130 kDa, Protein from Thermochaetoides thermophila)
- Dna strand 2 (70 kDa, DNA from synthetic construct)
- Dna (Complex from Synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Tetrafluoroaluminate ion (102 Da, Ligand)
INO80 core bound to hexasome composite map of state 2
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8oop
Q-score: 0.554
Zhang M, Jungblut A, Kunert F, Hauptmann L, Hoffmann T, Kolesnikova O, Metzner F, Moldt M, Weis F, DiMaio F, Hopfner KP, Eustermann S
Science (2023) 381 pp. 313-319 [ Pubmed: 37384673 DOI: doi:10.1126/science.adf6287 ]
- Actin-related protein 5 (87 kDa, Protein from Thermochaetoides thermophila)
- Ino80 core module in complex with hexasome (861 kDa, Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna strand 1 (69 kDa, DNA from synthetic construct)
- Chromatin-remodeling complex subunit ies6 (23 kDa, Protein from Thermochaetoides thermophila)
- Histones (Complex from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Ruvb-like protein 2 (53 kDa, Protein from Thermochaetoides thermophila)
- Histone h2a (14 kDa, Protein from Homo sapiens)
- Chromatin remodeler ino80 (Complex from Thermochaetoides thermophila)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Ruvb-like protein 1 (50 kDa, Protein from Thermochaetoides thermophila)
- Ino eighty subunit 2 (53 kDa, Protein from Thermochaetoides thermophila)
- Chromatin-remodeling atpase ino80 (130 kDa, Protein from Thermochaetoides thermophila)
- Dna strand 2 (70 kDa, DNA from synthetic construct)
- Dna (Complex from Synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Tetrafluoroaluminate ion (102 Da, Ligand)
CryoEM Structure INO80core Hexasome complex ATPase-hexasome refinement state 2
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 8oos
Q-score: 0.494
Zhang M, Jungblut A, Kunert F, Hauptmann L, Hoffmann T, Kolesnikova O, Metzner F, Moldt M, Weis F, DiMaio F, Hopfner KP, Eustermann S
Science (2023) 381 pp. 313-319 [ Pubmed: 37384673 DOI: doi:10.1126/science.adf6287 ]
- Chromatin-remodeling atpase ino80 (130 kDa, Protein from Thermochaetoides thermophila)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2a (14 kDa, Protein from Homo sapiens)
- Dna strand 1 (69 kDa, DNA from synthetic construct)
- Dna strand 2 (70 kDa, DNA from synthetic construct)
- Histones (Complex from Homo sapiens)
- Ino80 core module in complex with hexasome (861 kDa, Complex)
- Dna (Complex from Synthetic construct)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Ino80 (Complex from Thermochaetoides thermophila)
- Magnesium ion (24 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Tetrafluoroaluminate ion (102 Da, Ligand)