SMTL ID : 8x19.1

Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-1-1-1-1-3-3-2-1-1-1-mer

Ligands

7 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 16 residues within 4Å: Chain I: R.619, Q.622, M.645, G.646, G.648, K.649, T.650, I.651, E.685, R.688, W.689, N.2126, R.2154, I.2155 Ligands: MG.2, BEF.3 16 PLIP interactions: 16 interactions with chain I Hydrogen bonds: I:R.619, I:R.619, I:Q.622, I:Q.622, I:G.646, I:G.648, I:K.649, I:T.650, I:T.650, I:E.685, I:R.688, I:N.2126 Salt bridges: I:K.649, I:R.2154, I:R.2154 pi-Stacking: I:W.689 ADP.4: 18 residues within 4Å: Chain M: S.17, H.18, H.20, G.38, L.39, V.40, P.72, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, I.374, R.378, L.403, R.404 17 PLIP interactions: 17 interactions with chain M Hydrogen bonds: M:S.17, M:V.40, M:P.71, M:G.73, M:T.74, M:T.74, M:T.74, M:G.75, M:K.76, M:T.77, M:A.78, M:Y.366, M:Y.366 Salt bridges: M:H.18, M:K.76, M:R.404, M:R.404 ADP.5: 19 residues within 4Å: Chain N: A.24, H.25, H.27, I.28, G.45, M.46, V.47, P.79, G.80, T.81, G.82, K.83, T.84, A.85, N.329, Y.362, L.399, R.400, I.403 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:H.25, N:V.47, N:G.80, N:G.82, N:K.83, N:T.84, N:T.84, N:A.85, N:N.329, N:Y.362, N:Y.362 Salt bridges: N:H.25, N:K.83, N:R.400, N:R.400 ADP.6: 20 residues within 4Å: Chain O: H.18, H.20, G.38, L.39, V.40, G.41, P.71, P.72, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, I.374, L.403, R.404 Chain P: R.314, R.353 18 PLIP interactions: 15 interactions with chain O, 3 interactions with chain P Hydrogen bonds: O:V.40, O:G.41, O:G.73, O:T.74, O:G.75, O:K.76, O:T.77, O:T.77, O:A.78, O:Y.366, O:Y.366, P:R.314 Salt bridges: O:H.18, O:K.76, O:R.404, O:R.404, P:R.314, P:R.353 ADP.7: 21 residues within 4Å: Chain P: A.24, H.25, H.27, I.28, G.45, M.46, V.47, Q.78, P.79, G.80, T.81, G.82, K.83, T.84, A.85, N.329, Y.362, I.370, L.399, R.400, I.403 16 PLIP interactions: 16 interactions with chain P Hydrogen bonds: P:A.24, P:V.47, P:G.80, P:T.81, P:G.82, P:K.83, P:T.84, P:T.84, P:A.85, P:N.329, P:Y.362, P:Y.362 Salt bridges: P:H.25, P:K.83, P:R.400, P:R.400 ADP.8: 20 residues within 4Å: Chain Q: S.17, H.18, H.20, G.38, L.39, V.40, Q.42, P.72, G.73, T.74, G.75, K.76, T.77, A.78, N.332, Y.366, I.374, R.378, L.403, R.404 16 PLIP interactions: 16 interactions with chain Q Hydrogen bonds: Q:S.17, Q:V.40, Q:G.73, Q:T.74, Q:T.74, Q:G.75, Q:K.76, Q:T.77, Q:A.78, Q:N.332, Q:Y.366, Q:Y.366 Salt bridges: Q:H.18, Q:K.76, Q:R.404, Q:R.404 ADP.9: 19 residues within 4Å: Chain M: E.320 Chain R: A.24, H.25, H.27, G.45, M.46, V.47, P.79, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, I.370, L.399, R.400, I.403 17 PLIP interactions: 17 interactions with chain R Hydrogen bonds: R:A.24, R:V.47, R:G.80, R:T.81, R:T.81, R:T.81, R:G.82, R:K.83, R:T.84, R:T.84, R:A.85, R:Y.362, R:Y.362 Salt bridges: R:H.25, R:K.83, R:R.400, R:R.400

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain I: G.2124 Ligands: ADP.1, BEF.3 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:G.2124

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

BEF.3: 7 residues within 4Å: Chain I: M.645, G.646, K.649, E.747, R.2154 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP)

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.10: 17 residues within 4Å: Chain T: G.19, S.20, Y.21, T.22, R.24, G.173, A.174, G.199, Q.260, Q.263, A.264, G.352, G.353, N.354, L.356, I.357, R.390 9 PLIP interactions: 9 interactions with chain T Hydrogen bonds: T:S.20, T:Y.21, T:T.22, T:A.174, T:G.199, T:G.353 Salt bridges: T:R.24, T:R.24, T:R.390 ATP.11: 20 residues within 4Å: Chain U: G.13, S.14, G.15, M.16, K.18, Q.137, G.156, D.157, G.158, V.159, A.181, G.182, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 17 PLIP interactions: 17 interactions with chain U Hydrogen bonds: U:G.13, U:G.13, U:S.14, U:G.15, U:M.16, U:Q.137, U:D.157, U:D.157, U:G.158, U:V.159, U:E.214, U:E.214, U:G.302, U:T.303 Salt bridges: U:K.18, U:K.18, U:K.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, J. et al., Structural insights into histone exchange by human SRCAP complex. Cell Discov (2024)

Release Date

2024-03-06

Peptides

Histone H2A type 1-C: AE
Histone H2B type 1-C/E/F/G/I: BF
Histone H3.1: CG
Histone H4: DH
Helicase SRCAP: I
Vacuolar protein sorting-associated protein 72 homolog: J
Actin-related protein 6: K
Zinc finger HIT domain-containing protein 1: L
RuvB-like 1: MOQ
RuvB-like 2: NPR
Actin, cytoplasmic 1: SU
Actin-like protein 6A: T
DNA methyltransferase 1-associated protein 1: V
YEATS domain-containing protein 4: W

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

I
I

J
J

K
K

L
L

M
M

O
O

Q
Q

N
N

P
P

R
R

S
S

U
U

T
T

V
V

W
W

Histone H2A type 1-C

Histone H2B type 1-C/E/F/G/I

Histone H3.1

Histone H4

Helicase SRCAP

Vacuolar protein sorting-associated protein 72 homolog

Actin-related protein 6

Zinc finger HIT domain-containing protein 1

RuvB-like 1

RuvB-like 2

Actin, cytoplasmic 1

Actin-like protein 6A

DNA methyltransferase 1-associated protein 1

YEATS domain-containing protein 4

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