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SMTL ID : 6v2k.1

The nucleosome structure after H2A-H2B exchange

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1:	3 residues within 4Å: Chain A: M.124, P.125, K.126 Ligand excluded by PLIP
CL.2:	6 residues within 4Å: Chain C: G.48, A.49, G.50, A.51 Chain D: T.94, S.95 Ligand excluded by PLIP
CL.4:	2 residues within 4Å: Chain E: P.125, K.126 Ligand excluded by PLIP
CL.5:	7 residues within 4Å: Chain G: G.48, A.49, G.50, A.51 Chain H: T.94, S.95 Chain I: A.111 Ligand excluded by PLIP

10 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.3:	2 residues within 4Å: Chain E: Q.80, D.81 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.81
MN.6:	2 residues within 4Å: Chain I: C.26, A.27 No protein-ligand interaction detected (PLIP)
MN.7:	1 residues within 4Å: Chain I: G.134 No protein-ligand interaction detected (PLIP)
MN.8:	2 residues within 4Å: Chain I: G.68 Chain J: G.78 No protein-ligand interaction detected (PLIP)
MN.9:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.10:	1 residues within 4Å: Chain I: G.121 No protein-ligand interaction detected (PLIP)
MN.11:	1 residues within 4Å: Chain J: G.134 No protein-ligand interaction detected (PLIP)
MN.12:	1 residues within 4Å: Chain J: G.121 No protein-ligand interaction detected (PLIP)
MN.13:	3 residues within 4Å: Chain I: C.107 Chain J: G.39, G.40 No protein-ligand interaction detected (PLIP)
MN.14:	2 residues within 4Å: Chain J: G.71, A.72 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Hirano, R. et al., Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome. Commun Biol (2021)

Release Date

2020-11-25

Peptides

Histone H3.1: AE
Histone H4: BF
Histone H2A: CG
Histone H2B type 1-J: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Histone H3.1

Histone H4

Histone H2A

Histone H2B type 1-J

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