Uniprot accession / id : P84228  OR   Uniprot accession / id : Q71DI3
 
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Latest PDB release
Entries released this week  (1)
revised
(10)
 
Entry Information
Entry status  (1)
REL
(107)
 
Experimental methods  (3)
Electron Microscopy
(78)
X-ray diffraction
(28)
Solution NMR
(1)
 
Authors  (361)
Cramer P
(28)
Dienemann C
(28)
Dodonova S
(23)
Dombrowski M
(23)
Engeholm M
(23)
Freudenthal BD
(16)
Weaver TM
(16)
Ai HS
(10)
Liu L
(10)
Deng Z
(9)
Li JB
(9)
Liang L
(9)
Sun M
(9)
Tong Z
(9)
Ai H
(8)
Gozani O
(8)
Kuo AJ
(8)
Ryan BJ
(8)
Patel DJ
(7)
Shi Q
(7)
Cheng Z
(6)
Cheng ZJ
(6)
Cheung P
(6)
Kurumizaka H
(6)
Li H
(6)
Pan M
(6)
Wilmot CM
(6)
Yukl ET
(6)
Dodonova SO
(5)
McGinty RK
(5)
Spangler CJ
(5)
Su X
(5)
Taipale J
(5)
Zhu F
(5)
Cookis T
(4)
Cordero C
(4)
Cortez D
(4)
Deng ZH
(4)
Fierz B
(4)
Gakhar L
(4)
Hoitsma NM
(4)
Kasinath V
(4)
Li Z
(4)
Ling JA
(4)
Lydecker A
(4)
Mehta KPM
(4)
Nogales E
(4)
Roberts SA
(4)
Sauer P
(4)
Schnicker NJ
(4)
Spencer JJ
(4)
Tong ZB
(4)
Xu P
(4)
Zheng Q
(4)
Ablasser A
(3)
Allen MD
(3)
Arteaga EC
(3)
Azzam DN
(3)
Bonadies N
(3)
Budziszewski GR
(3)
Bycroft M
(3)
Cao L
(3)
Cesmat AP
(3)
Chu G
(3)
Deng H
(3)
Ding X
(3)
Dou Y
(3)
Du Y
(3)
Eustermann S
(3)
Freund SM
(3)
Freund SMV
(3)
Gao S
(3)
Gottgens B
(3)
Guey B
(3)
Göttgens B
(3)
Hopfner KP
(3)
Horikoshi N
(3)
Huntly BJ
(3)
Huntly BJP
(3)
Jing T
(3)
Kireev D
(3)
Kostrewa D
(3)
Kvinlaug B
(3)
Kvinlaug BT
(3)
Lee SY
(3)
Lei Y
(3)
Li P
(3)
Liang J
(3)
Liu A
(3)
Liu AJ
(3)
Liu T
(3)
Liu WR
(3)
Liu Y
(3)
Lou Z
(3)
Lou ZY
(3)
Man P
(3)
Melenec P
(3)
Moldt M
(3)
Qu Q
(3)
Rowlett CM
(3)
 
More...
 
Homo / hetero assembly  (1)
hetero
(107)
 
Assembly composition  (3)
DNA/protein complex
(81)
protein/protein complex
(25)
DNA/RNA hybrid/protein complex
(1)
 
Assembly polymer count  (16)
undecamer
(30)
decamer
(20)
dimer
(17)
dodecamer
(14)
trimer
(7)
icosamer
(3)
tetradecamer
(3)
tridecamer
(3)
28-mer
(2)
nonadecamer
(2)
22-mer
(1)
27-mer
(1)
29-mer
(1)
36-mer
(1)
octadecamer
(1)
tetramer
(1)
 
Resolution distribution
1.0 - 1.5
(1)
1.5 - 2
(12)
2.0 - 2.5
(12)
2.5 - 3
(8)
3.0 - 3.5
(31)
3.5 - 4
(12)
4.0 - 4.5
(13)
4.5 - 5
(3)
5.0 - 5.5
(4)
5.5 - 6
(1)
6.0 - 6.5
(1)
6.5 - 7
(1)
7.0 - 7.5
(1)
7.5 - 8
(1)
9.0 - 9.5
(1)
9.5 - 10
(3)
10.5 - 11
(1)
 
Release year distribution
2005 - 2010
(7)
2010 - 2015
(16)
2015 - 2020
(22)
2020 - 2025
(80)
2025 - 2030
(14)
 
Journal  (20)
Nat Struct Mol Biol
(34)
Nature
(12)
To be published
(11)
Nat Commun
(10)
Genes Dev
(9)
Nat Chem Biol
(5)
Nucleic Acids Res
(4)
Biorxiv
(3)
J Biol Chem
(3)
Biochem Biophys Res Commun
(2)
Proc Natl Acad Sci U S A
(2)
Sci Adv
(2)
Science
(2)
Structure
(2)
Acta Crystallogr D Biol Crystallogr
(1)
Chem
(1)
J Struct Biol
(1)
Mol Cell
(1)
Mol Cell Proteomics
(1)
PLoS One
(1)
 
Macromolecules
Organism superkingdom  (1)
Eukaryota
(106)
 
Organism name  (4)
Homo sapiens
(97)
Mus musculus
(8)
Xenopus laevis
(1)
synthetic construct
(1)
 
Molecule name  (11)
H3-clustered histone 13
(107)
H3-clustered histone 14
(107)
H3-clustered histone 15
(107)
Histone H3.2
(107)
Histone H3/m
(99)
Histone H3/o
(99)
H3-clustered histone 2
(8)
H3-clustered histone 3
(8)
H3-clustered histone 4
(8)
H3-clustered histone 6
(8)
H3-clustered histone 7
(8)
 
Molecule type  (1)
Protein
(107)
 
Gene names  (37)
H3C13
(99)
H3C14
(99)
H3C15
(99)
H3F2
(99)
H3FM
(99)
HIST2H3A
(99)
HIST2H3C
(99)
HIST2H3D
(99)
H3-143
(8)
H3-53
(8)
H3-B
(8)
H3-F
(8)
H3.2
(8)
H3.2-221
(8)
H3.2-614
(8)
H3.2-615
(8)
H3.2-616
(8)
H3b
(8)
H3c13
(8)
H3c14
(8)
H3c15
(8)
H3c2
(8)
H3c3
(8)
H3c4
(8)
H3c6
(8)
H3c7
(8)
H3f
(8)
Hist1h3b
(8)
Hist1h3c
(8)
Hist1h3d
(8)
Hist1h3e
(8)
Hist1h3f
(8)
Hist2h3b
(8)
Hist2h3c1
(8)
Hist2h3c2
(8)
Hist2h3ca1
(8)
Hist2h3ca2
(8)
 
Interacting Molecules  (107)
Histone H4
(83)
Histone H2A type 1-B/E
(44)
Histone H2B type 1-K
(41)
Histone H2A type 1
(28)
Histone H2B type 1-C/E/F/G/I
(26)
Histone H1.4
(18)
DNA (145-MER)
(10)
601 J strand (non-damaged strand)
(9)
Histone H2B type 1-J
(9)
601 I strand (damaged strand 1)
(8)
601 K strand (damaged strand 2)
(8)
Cyclic GMP-AMP synthase
(8)
Lysine-specific demethylase 2A
(8)
DNA (147-MER)
(7)
Ubiquitin
(7)
DNA (146-MER)
(6)
DNA (167-MER)
(6)
Ubiquitin-conjugating enzyme E2 D3
(6)
DNA polymerase beta
(5)
Spindlin-1
(5)
DNA (157-MER)
(4)
DNA (177-MER)
(4)
E3 ubiquitin-protein ligase RNF168
(4)
Histone H2A type 2-A
(4)
DNA (144-MER)
(3)
Histone H2A
(3)
Histone H2B 1.1
(3)
INO80 complex subunit B-like conserved region domain-containing protein
(3)
Peregrin
(3)
Transcription factor SOX-11
(3)
601 I strand (damaged strand)
(2)
601 I strand (non-damaged strand)
(2)
601 J strand (damaged strand)
(2)
BRCA1-associated RING domain protein 1
(2)
Breast cancer type 1 susceptibility protein
(2)
DNA
(2)
DNA (153-MER)
(2)
DNA (591-MER)
(2)
Histone H2B
(2)
Histone-lysine N-methyltransferase, H3 lysine-79 specific
(2)
Ino80
(2)
N-glycosylase/DNA lyase
(2)
NAD-dependent protein deacetylase sirtuin-7
(2)
RuvB-like helicase
(2)
V(D)J recombination-activating protein 2
(2)
Vps72/YL1 C-terminal domain-containing protein
(2)
146-MER DNA
(1)
601 J strand (non-damaged)
(1)
Actin related protein 5
(1)
DASH complex subunit DAD4
(1)
DNA (136-MER)
(1)
DNA (137-MER)
(1)
DNA (143-MER)
(1)
DNA (148-MER)
(1)
DNA (149-MER)
(1)
DNA (151-MER)
(1)
DNA (171-MER)
(1)
DNA (172-MER)
(1)
DNA (176-MER)
(1)
DNA (182-MER)
(1)
DNA (185-MER)
(1)
DNA (202-MER)
(1)
DNA (203-MER)
(1)
DNA (208-MER)
(1)
DNA (226-MER)
(1)
DNA (227-MER)
(1)
DNA (520-MER)
(1)
DNA (522-MER)
(1)
DNA (541-MER)
(1)
DNA (561-MER)
(1)
DNA (563-MER)
(1)
DNA (702-MER)
(1)
DNA (788-MER)
(1)
DNA (cytosine-5)-methyltransferase 3B
(1)
DNA (natural)
(1)
DNA repair nuclease/redox regulator APEX1
(1)
DNA replication licensing factor MCM2
(1)
DNA/RNA (185-MER)
(1)
E3 ubiquitin-protein ligase UHRF1
(1)
Elongin-B
(1)
Elongin-C
(1)
Histone H1.0
(1)
Histone H1.0-B
(1)
Histone H2A type 1-H
(1)
Histone H2A type 1-J
(1)
Histone H2A type 2-C
(1)
Histone H2A.Z
(1)
Histone H2B type 1-H
(1)
Histone H2B type 1-N
(1)
Histone H3.2
(1)
Histone chaperone ASF1A
(1)
Histone chaperone ASF1B
(1)
Histone-lysine N-methyltransferase KMT5B
(1)
Ino80 ATPase
(1)
M-phase phosphoprotein 8
(1)
NAD-dependent protein deacylase sirtuin-5, mitochondrial
(1)
Nucleosomal DNA Strand 1
(1)
Nucleosomal DNA Strand 2
(1)
Probable Histone-lysine N-methyltransferase ATXR5
(1)
Protein SSX1
(1)
 
More...
 
Interacting ligands  (12)
AKG : 2-OXOGLUTARIC ACID
(3)
OGA : N-OXALYLGLYCINE
(3)
GOL : GLYCEROL
(2)
MN : MANGANESE (II) ION
(2)
OH0 : N-heptanoyl-N-hydroxy-beta-alanine
(2)
PTD : PENTANEDIAL
(2)
SAM : S-ADENOSYLMETHIONINE
(2)
A1IY0 : [[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
(1)
CL : CHLORIDE ION
(1)
MRD : (4R)-2-METHYLPENTANE-2,4-DIOL
(1)
SAH : S-ADENOSYL-L-HOMOCYSTEINE
(1)
SO4 : SULFATE ION
(1)
 
Function and Biology
Biological function  (5)
DNA binding
(83)
structural constituent of chromatin
(70)
protein heterodimerization activity
(69)
chromatin binding
(68)
protein binding
(68)
 
Representative Structures
Representative Structures
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Entries 1 to 10 of 107
Entries 1 to 10 of 107
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Cryo-EM structure of SSX1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom
Zebin T, Ai HS, Ziyu X, Man P, Liu L
Nat Struct Mol Biol (2024) [PMID: 38177667  ]
Source organism: Homo sapiens  
Assembly composition: DNA/protein complex
PDBe complex ID: PDB-CPX-270501 (Preferred)   search this ID
PDBe-KB: Q71DI3    Q16384    P62805    O60814    P04908   
Electron Microscopy
3.02Å resolution
Released: 13 Sep 2023
Model geometry
Fit model/data
Data not analysed
8hr1
8hr1
8hr1
Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom
Zebin T, Ai HS, Ziyu X, GuoChao C, Man P, Liu L
Nat Struct Mol Biol (2024) [PMID: 38177667  ]
Source organism: Homo sapiens  
Assembly composition: DNA/protein complex
PDBe complex ID: PDB-CPX-270500 (Preferred)   search this ID
PDBe-KB: Q71DI3    P0CG47    Q16385    P62805    O60814    P04908   
Electron Microscopy
3.05Å resolution
Released: 27 Sep 2023
Model geometry
Fit model/data
Data not analysed
8hqy
8hqy
8hqy
Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex
Zhao F, Li H
J Biol Chem (2020) [PMID: 32994220  ]
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Modified residues: M3L    MLY    MLY    M3L   
Assembly name: Histone H3.2 and Spindlin-1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-180745 (Preferred)   search this ID
PDBe-KB: Q71DI3    Q9Y657   
X-ray diffraction
3.502Å resolution
Released: 14 Oct 2020
Model geometry
Fit model/data
7bu9
7bu9
7bu9
Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
Bergamin E, Sarvan S, Malette J, Eram M, Yeung S, Mongeon V, Joshi M, Brunzelle JS, Michaels SD, Blais A, Vedadi M, Couture JF
Nucleic Acids Res (2017) [PMID: 28383693  ]
Assembly composition: protein/protein complex
Bound ligands: DMS    SAH    DMS    SAH   
Assembly name: Probable Histone-lysine N-methyltransferase ATXR5 and Histone H3.2 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-110885 (Preferred)   search this ID
PDBe-KB: Q71DI3    B9RU15   
X-ray diffraction
1.949Å resolution
Released: 19 Apr 2017
Model geometry
Fit model/data
5vac
5vac
5vac
The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
Suzuki Y, Horikoshi N, Kato D, Kurumizaka H
Biochem Biophys Res Commun (2016) [PMID: 26694698  ]
Source organism: Homo sapiens  
Assembly composition: DNA/protein complex
Bound ligands: MN    CL    MN   
Assembly name: Nucleosome, variant H3.2-H2A.2-H2B.1 and DNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-118413 (Preferred)   search this ID
PDBe-KB: Q71DI3    P62805    P06899    P04908   
X-ray diffraction
1.987Å resolution
Released: 27 Jan 2016
Model geometry
Fit model/data
5b0z
5b0z
5b0z
Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.2-H4 dimer
Huang H, Patel DJ
Nat Struct Mol Biol (2015) [PMID: 26167883  ]
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Bound ligands: GOL   
PDBe complex ID: PDB-CPX-156000 (Preferred)   search this ID
PDBe-KB: Q71DI3    P49736    P62805    Q9NVP2   
X-ray diffraction
2.906Å resolution
Released: 17 Jun 2015
Model geometry
Fit model/data
5bo0
5bo0
5bo0
Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122
Suzuki Y, Horikoshi N, Kurumizaka H
Biochem Biophys Res Commun (2016) [PMID: 26694698  ]
Source organism: Homo sapiens  
Assembly composition: DNA/protein complex
Bound ligands: MN    CL    MN   
Modified residues: KCR    KCR   
Assembly name: Nucleosome, variant H3.2-H2A.2-H2B.1 and DNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-118412 (Preferred)   search this ID
PDBe-KB: Q71DI3    P62805    P06899    P04908   
X-ray diffraction
2.557Å resolution
Released: 27 Jan 2016
Model geometry
Fit model/data
5b0y
5b0y
5b0y
Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain
Rondelet G, DAL MASO T, Willems L, Wouters J
J Struct Biol (2016) [PMID: 26993463  ]
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Bound ligands: GOL   
Modified residues: M3L    M3L   
Assembly name: Histone H3.2 and DNA (cytosine-5)-methyltransferase 3B (Preferred)   search this complex
PDBe complex ID: PDB-CPX-180743 (Preferred)   search this ID
PDBe-KB: Q71DI3    Q9UBC3   
X-ray diffraction
2.24Å resolution
Released: 30 Mar 2016
Model geometry
Fit model/data
5ciu
5ciu
5ciu
Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome
Witus SR, Burrell AL, Hansen JM, Farrell DP, Dimaio F, Kollman JM, Klevit RE
Nat Struct Mol Biol (2021) [PMID: 33589814  ]
Assembly composition: DNA/protein complex
Bound ligands: ZN    ZN   
PDBe complex ID: PDB-CPX-121415 (Preferred)   search this ID
PDBe-KB: Q71DI3    P38398    Q99728    Q6FI13    O60814    P62805    (view 1 more)
Electron Microscopy
3.9Å resolution
Released: 17 Feb 2021
Model geometry
Fit model/data
Data not analysed
7jzv
7jzv
7jzv
cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure)
Xu PB, Ablasser A
Nature (2024) [PMID: 38418882  ]
Source organism: Homo sapiens  
Assembly composition: DNA/protein complex
Bound ligands: ZN    ZN   
PDBe complex ID: PDB-CPX-270612 (Preferred)   search this ID
PDBe-KB: Q71DI3    Q6PJ21    Q99878    Q15369    Q99877    Q15370    (view 4 more)
Electron Microscopy
3.5Å resolution
Released: 14 Feb 2024
Model geometry
Fit model/data
Data not analysed
8ol1
8ol1
8ol1
...
Entries 1 to 10 of 107
Entries 1 to 10 of 107