SMTL ID : 7vdv.1

The overall structure of human chromatin remodeling PBAF-nucleosome complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-1-1-1-1-1-1-1-2-1-1-1-1-mer

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK: unknown(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 4 residues within 4Å: Chain J: A.235 Chain O: Y.610, G.611, V.612 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain O Hydrophobic interactions: J:A.235, O:Y.610

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 8 residues within 4Å: Chain J: M.623, K.627, G.1004, L.1005, R.1031, R.1034 Ligands: MG.3, ADP.4 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain J: K.627, T.628 Ligands: BEF.2, ADP.4 No protein-ligand interaction detected (PLIP)

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.4: 17 residues within 4Å: Chain J: V.595, Q.600, E.622, M.623, G.624, L.625, G.626, K.627, T.628, I.629, W.667, N.1006, Q.1008, R.1034, I.1035 Ligands: BEF.2, MG.3 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:V.595, J:Q.600, J:E.622, J:G.626, J:K.627, J:I.629, J:N.1006, J:Q.1008 Salt bridges: J:K.627, J:R.1034, J:R.1034

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, J.J. et al., Structure of human chromatin-remodelling PBAF complex bound to a nucleosome. Nature (2022)

Release Date

2022-05-18

Peptides

Histone H4: AE
Histone H2A: BF
Histone H2B 1.1: CG
Histone H3: DV
Isoform 2 of Transcription activator BRG1: J
Actin-like protein 6A: K
Actin, cytoplasmic 1: L
AT-rich interactive domain-containing protein 2,AT-rich interactive domain-containing protein 2: M
PHD finger protein 10: N
Isoform 2 of Bromodomain-containing protein 7: O
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1: P
SWI/SNF complex subunit SMARCC2: QR
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1: S
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1: T
Protein polybromo-1: U
unknown: W

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E
F

B
C

F
G

C
D

G
H

D
E

V
K

J
A

K
N

L
P

M
Q

N
R

O
T

P
V

Q
W

R
X

S
Y

T
Z

U
a

W
M

Histone H4

Histone H2A

Histone H2B 1.1

Histone H3

Isoform 2 of Transcription activator BRG1

Actin-like protein 6A

Actin, cytoplasmic 1

AT-rich interactive domain-containing protein 2,AT-rich interactive domain-containing protein 2

PHD finger protein 10

Isoform 2 of Bromodomain-containing protein 7

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1

SWI/SNF complex subunit SMARCC2

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1

Protein polybromo-1

unknown

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