Structural basis for the linker histone H5-nucleosome binding and chromatin compaction
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8xjv
Q-score: 0.424
Li W, Hu J, Song F, Yu J, Peng X, Zhang S, Wang L, Hu M, Liu JC, Wei Y, Xiao X, Li Y, Li D, Wang H, Zhou BR, Dai L, Mou Z, Zhou M, Zhang H, Zhou Z, Zhang H, Bai Y, Zhou JQ, Li W, Li G, Zhu P
Cell Res (2024) 34 pp. 707-724 [ DOI: doi:10.1038/s41422-024-01009-z Pubmed: 39103524 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2b (Complex from Xenopus laevis)
- Linker histone h5 (Complex from Gallus gallus)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h5 (21 kDa, Protein from Gallus gallus)
- Dna (660 kDa, DNA from synthetic construct)
- 12x177bp-h5 chromatin (Complex)
- Dna (651 kDa, DNA from synthetic construct)
- Histone h3.1 (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (Complex from synthetic construct)
- Histone h2a (Complex from Xenopus laevis)
Structure of human APC3loop 375-381 bound to the NCP
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 9fgq
Q-score: 0.651
Cirillo L, Young R, Veerapathiran S, Roberti A, Martin M, Abubacar A, Perosa C, Coates C, Muhammad R, Roumeliotis TI, Choudhary JS, Alfieri C, Pines J
EMBO J (2024) 43 pp. 4324-4355 [ Pubmed: 39143240 DOI: doi:10.1038/s44318-024-00194-2 ]
- Histone h2a type 2-a (14 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-b (29 kDa, Protein from Homo sapiens)
- Dna (132-mer) (64 kDa, DNA from Homo sapiens)
- Cell division cycle protein 27 homolog (32 kDa, Protein from Homo sapiens)
- Dna (131-mer) (65 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Apc3 motif bound to the ncp acidic patch (Complex from Homo sapiens)
Cryo-EM structure of nucleosome containing Arabidopsis thaliana histones
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8j91
Q-score: 0.545
Osakabe A, Takizawa Y, Horikoshi N, Hatazawa S, Negishi L, Sato S, Berger F, Kakutani T, Kurumizaka H
Nat Commun (2024) 15 pp. 5187-5187 [ DOI: doi:10.1038/s41467-024-49465-w Pubmed: 38992002 ]
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Dna (169-mer) (51 kDa, DNA from synthetic construct)
- Hta13 (14 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Nucleosome containing arabidopsis thaliana histones (200 kDa, Complex from Arabidopsis thaliana)
Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8b0a
Q-score: 0.483
Bacic L, Gaullier G, Mohapatra J, Mao G, Brackmann K, Panfilov M, Liszczak G, Sabantsev A, Deindl S
Nat Commun (2024) 15 pp. 1000-1000 [ Pubmed: 38307862 DOI: doi:10.1038/s41467-024-45237-8 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (98 kDa, Protein from Homo sapiens)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Complex between alc1 and a site-specifically parylated nucleosome (304 kDa, Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
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 [ DOI: doi:10.1126/science.adf6287 Pubmed: 37384673 ]
- Chromatin-remodeling atpase ino80 (130 kDa, Protein from Thermochaetoides thermophila)
- Dna strand 1 (69 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Chromatin-remodeling complex subunit ies6 (23 kDa, Protein from Thermochaetoides thermophila)
- Histones (Complex from Homo sapiens)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Histone h2a (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Ino eighty subunit 2 (53 kDa, Protein from Thermochaetoides thermophila)
- Ino80 core module in complex with hexasome (861 kDa, Complex)
- Ruvb-like protein 2 (53 kDa, Protein from Thermochaetoides thermophila)
- Dna (Complex from Synthetic construct)
- Chromatin remodeler ino80 (Complex from Thermochaetoides thermophila)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Actin-related protein 5 (87 kDa, Protein from Thermochaetoides thermophila)
- Dna strand 2 (70 kDa, DNA from synthetic construct)
- Ruvb-like protein 1 (50 kDa, Protein from Thermochaetoides thermophila)
CryoEM Structure INO80core Hexasome complex Hexasome refinement state1
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8ooa
Q-score: 0.525
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 [ DOI: doi:10.1126/science.adf6287 Pubmed: 37384673 ]
- Histone h2b (13 kDa, Protein from Homo sapiens)
- 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)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Ino80 core module in complex with hexasome (861 kDa, Complex from Thermochaetoides thermophila)
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 [ DOI: doi:10.1126/science.adf6287 Pubmed: 37384673 ]
- Chromatin-remodeling atpase ino80 (130 kDa, Protein from Thermochaetoides thermophila)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Chromatin-remodeling complex subunit ies6 (23 kDa, Protein from Thermochaetoides thermophila)
- Histones (Complex from Homo sapiens)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Histone h2a (14 kDa, Protein from Homo sapiens)
- Dna strand 1 (69 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Ino eighty subunit 2 (53 kDa, Protein from Thermochaetoides thermophila)
- Ino80 core module in complex with hexasome (861 kDa, Complex)
- Ruvb-like protein 2 (53 kDa, Protein from Thermochaetoides thermophila)
- Dna (Complex from Synthetic construct)
- Chromatin remodeler ino80 (Complex from Thermochaetoides thermophila)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Actin-related protein 5 (87 kDa, Protein from Thermochaetoides thermophila)
- Dna strand 2 (70 kDa, DNA from synthetic construct)
- Ruvb-like protein 1 (50 kDa, Protein from Thermochaetoides thermophila)
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 [ DOI: doi:10.1126/science.adf6287 Pubmed: 37384673 ]
- Histones (Complex from Homo sapiens)
- Chromatin-remodeling atpase ino80 (130 kDa, Protein from Thermochaetoides thermophila)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Histone h2a (14 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ino80 (Complex from Thermochaetoides thermophila)
- Ino80 core module in complex with hexasome (861 kDa, Complex)
- Dna strand 1 (69 kDa, DNA from synthetic construct)
- Dna strand 2 (70 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (Complex from Synthetic construct)
Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7ssa
Q-score: 0.449
Donovan BT, Chen H, Eek P, Meng Z, Jipa C, Tan S, Bai L, Poirier MG
Mol Cell (2023) 83 pp. 1251-1263.e6 [ DOI: doi:10.1016/j.molcel.2023.03.006 Pubmed: 36996811 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a.1 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Centromere-binding protein 1 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (137-mer) (46 kDa, DNA from synthetic construct)
- Centromere-binding protein 1 (39 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h3.2, histone h4 (Complex from Xenopus laevis)
- Dna (137-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a.1, histone h2b.1 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (Complex from synthetic construct)
- Pioneer factor cbf1 in complex with the nucleosome (286 kDa, Complex)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7v90
Q-score: 0.459
Soman A, Wong SY, Korolev N, Surya W, Lattmann S, Vogirala VK, Chen Q, Berezhnoy NV, van Noort J, Rhodes D, Nordenskiold L
Nature (2022) 609 pp. 1048-1055 [ DOI: doi:10.1038/s41586-022-05236-5 Pubmed: 36104563 ]
- Telomeric mononucleosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (145-mer) (43 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (145-mer) (46 kDa, DNA from Homo sapiens)
- Histone h2b type 1-k (11 kDa, Protein from Homo sapiens)