SMTL ID : 9hwg.1

Structure of the transcribing Pol II-TCR-RECQL5 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.71, C.74, C.81, P.82, H.84 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.71, A:C.74, A:C.81, A:H.84 ZN.2: 5 residues within 4Å: Chain A: C.111, C.114, C.154, C.184, Q.188 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.154 ZN.4: 4 residues within 4Å: Chain B: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1119, B:C.1122, B:C.1137, B:C.1140 ZN.5: 4 residues within 4Å: Chain C: C.88, C.90, C.94, C.97 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.88, C:C.90, C:C.94, C:C.97 ZN.6: 5 residues within 4Å: Chain I: C.17, C.20, C.39, N.41, C.42 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.39 ZN.7: 4 residues within 4Å: Chain I: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.86, I:C.89, I:C.114, I:C.119 ZN.8: 4 residues within 4Å: Chain J: C.7, C.10, 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: 4 residues within 4Å: Chain L: C.19, C.22, C.36, C.39 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.19, L:C.22, L:C.36, L:C.39 ZN.10: 4 residues within 4Å: Chain N: I.542, R.550, F.588, Y.597 No protein-ligand interaction detected (PLIP) ZN.12: 4 residues within 4Å: Chain U: C.26, C.29, C.50, C.53 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.26, U:C.29, U:C.50, U:C.53

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.495, D.497, D.499 Chain O: A.45 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.499 MG.11: 2 residues within 4Å: Chain R: T.539, D.646 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Structural basis of RECQL5-induced RNA polymerase II transcription braking and subsequent reactivation. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-07-16

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase II subunit RPB3: C
RNA polymerase II subunit D: D
DNA-directed RNA polymerase II subunit E: E
DNA-directed RNA polymerases I, II, and III subunit RPABC2: F
DNA-directed RNA polymerase subunit: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase II subunit RPB9: I
DNA-directed RNA polymerases I, II, and III subunit RPABC5: J
DNA-directed RNA polymerase II subunit RPB11-a: K
RNA polymerase II, I and III subunit K: L
ATP-dependent DNA helicase Q5: N
DNA excision repair protein ERCC-8: Q
DNA excision repair protein ERCC-6: R
UV-stimulated scaffold protein A: S
DNA damage-binding protein 1: T
Transcription elongation factor 1 homolog: U

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

N
O

Q
a

R
b

S
c

T
d

U
e

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

RNA polymerase II subunit D

DNA-directed RNA polymerase II subunit E

DNA-directed RNA polymerases I, II, and III subunit RPABC2

DNA-directed RNA polymerase subunit

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

DNA-directed RNA polymerase II subunit RPB9

DNA-directed RNA polymerases I, II, and III subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11-a

RNA polymerase II, I and III subunit K

ATP-dependent DNA helicase Q5

DNA excision repair protein ERCC-8

DNA excision repair protein ERCC-6

UV-stimulated scaffold protein A

DNA damage-binding protein 1

Transcription elongation factor 1 homolog

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