SMTL ID : 9ehz.1

Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.60 Å

Oligo State

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

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain F: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.17, F:C.20, F:C.39, F:C.42 ZN.2: 4 residues within 4Å: Chain F: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.86, F:C.89, F:C.114, F:C.119 ZN.3: 5 residues within 4Å: Chain G: C.7, C.10, R.42, C.44, C.45 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.7, G:C.10, G:C.44, G:C.45 ZN.4: 4 residues within 4Å: Chain I: C.19, C.22, C.36, C.39 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.19, I:C.22, I:C.36, I:C.39 ZN.6: 5 residues within 4Å: Chain M: C.71, T.73, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.71, M:C.74, M:C.81, M:H.84 ZN.7: 5 residues within 4Å: Chain M: C.111, C.114, C.154, G.183, C.184 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.111, M:C.114, M:C.154, M:C.184 ZN.8: 4 residues within 4Å: Chain N: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.1119, N:C.1122, N:C.1137, N:C.1140 ZN.9: 4 residues within 4Å: Chain O: C.88, C.90, C.94, C.97 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.88, O:C.90, O:C.94, O:C.97

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain K: C.20 Chain M: D.495, D.497, D.499 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:D.495, M:D.497, M:D.499, M:D.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ariza, A.J.F. et al., Structural insights into transcriptional regulation by the helicase RECQL5. Biorxiv (2025)

Release Date

2025-03-05

Peptides

DNA-directed RNA polymerase II subunit RPB4: A
DNA-directed RNA polymerases I, II, and III subunit RPABC1: B
DNA-directed RNA polymerases I, II, and III subunit RPABC2: C
DNA-directed RNA polymerase II subunit RPB7: D
DNA-directed RNA polymerases I, II, and III subunit RPABC3: E
DNA-directed RNA polymerase II subunit RPB9: F
DNA-directed RNA polymerases I, II, and III subunit RPABC5: G
DNA-directed RNA polymerase II subunit RPB11-a: H
DNA-directed RNA polymerases I, II, and III subunit RPABC4: I
DNA-directed RNA polymerase II subunit RPB1: M
DNA-directed RNA polymerase II subunit RPB2: N
DNA-directed RNA polymerase II subunit RPB3: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
G

E
H

F
I

G
J

H
K

I
L

M
A

N
B

O
C

DNA-directed RNA polymerase II subunit RPB4

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

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

DNA-directed RNA polymerase II subunit RPB7

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

DNA-directed RNA polymerases I, II, and III subunit RPABC4

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase II subunit RPB2

DNA-directed RNA polymerase II subunit RPB3

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