SMTL ID : 7wbx.1

RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: G.59, C.67, T.69, C.70, C.77, P.78, H.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.70, A:C.77, A:H.80 ZN.2: 7 residues within 4Å: Chain A: C.107, N.109, C.110, G.111, C.148, G.167, C.168 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.168 ZN.4: 5 residues within 4Å: Chain B: C.1163, I.1165, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1163, B:C.1166, B:C.1182, B:C.1185 ZN.5: 5 residues within 4Å: Chain C: C.85, C.87, Y.90, C.91, C.94 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.85, C:C.87, C:C.91, C:C.94 ZN.6: 6 residues within 4Å: Chain I: C.75, C.78, C.103, L.104, N.105, C.106 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.75, I:C.78, I:C.103 ZN.7: 5 residues within 4Å: Chain I: C.7, C.10, N.12, C.29, C.32 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.10, I:C.29, I:C.32 ZN.8: 8 residues within 4Å: Chain J: C.7, S.9, C.10, G.11, K.12, R.42, C.44, C.45 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.44, J:C.45 ZN.9: 7 residues within 4Å: Chain L: C.33, C.36, A.37, C.50, E.52, C.53, H.55 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.33, L:C.36, L:C.50, L:C.53 ZN.10: 6 residues within 4Å: Chain M: C.28, C.31, S.36, C.52, C.55, L.57 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.28, M:C.31, M:C.52, M:C.55 ZN.11: 8 residues within 4Å: Chain Q: C.6, L.8, C.9, I.11, C.23, N.25, C.26, L.30 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.6, Q:C.9, Q:C.23, Q:C.26

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: R.447, D.482, D.484, D.486 Chain O: G.16 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.482, A:D.484, A:D.486, A:D.486

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osumi, K. et al., Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome. J.Mol.Biol. (2023)

Release Date

2023-07-05

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
RNA polymerase II third largest subunit B44, part of central core: C
RNA polymerase II subunit B32: D
DNA-directed RNA polymerases I, II, and III subunit RPABC1: E
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III: F
RNA polymerase II subunit: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase subunit: I
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III: J
RNA polymerase II subunit B12.5: K
RNA polymerase subunit ABC10-alpha: L
Transcription elongation factor 1 homolog: M
Transcription elongation factor SPT4: Q
Transcription elongation factor SPT5: R
Histone H3.3: SW
Histone H4: TX
Histone H2A type 1-B/E: UY
Histone H2B type 1-J: VZ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

Q
V

R
W

S
a

W
e

T
b

X
f

U
c

Y
g

V
d

Z
h

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

RNA polymerase II third largest subunit B44, part of central core

RNA polymerase II subunit B32

DNA-directed RNA polymerases I, II, and III subunit RPABC1

RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III

RNA polymerase II subunit

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase subunit

RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III

RNA polymerase II subunit B12.5

RNA polymerase subunit ABC10-alpha

Transcription elongation factor 1 homolog

Transcription elongation factor SPT4

Transcription elongation factor SPT5

Histone H3.3

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

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