SMTL ID : 9ei3.1

Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.71, T.73, C.74, C.81, H.84 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.71, A:T.73, A:C.74, A:C.81, A:H.84 ZN.2: 4 residues within 4Å: Chain A: C.111, C.114, C.154, C.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.154, A:C.184 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: 4 residues within 4Å: Chain I: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.39, I:C.42 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: 5 residues within 4Å: Chain J: C.7, C.10, 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: 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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.495, D.497, D.499 Chain N: C.20 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.495, A:D.495, A:D.497

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.10: 14 residues within 4Å: Chain P: F.26, S.28, F.29, K.30, Q.34, M.52, P.53, T.54, G.55, A.56, E.158, V.323, Q.345, R.352 10 PLIP interactions: 10 interactions with chain P Hydrogen bonds: P:F.29, P:K.30, P:Q.34, P:Q.34, P:P.53, P:A.56, P:E.158, P:E.158, P:E.158, P:V.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Florez Ariza, A.J. et al., Structural insights into transcriptional regulation by the helicase RECQL5. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-03-05

Peptides

DNA-directed RNA polymerase II subunit RPB1: A
DNA-directed RNA polymerase II subunit RPB2: B
DNA-directed RNA polymerase II subunit RPB3: C
DNA-directed RNA polymerase II subunit RPB4: D
DNA-directed RNA polymerases I, II, and III subunit RPABC1: E
DNA-directed RNA polymerases I, II, and III subunit RPABC2: F
DNA-directed RNA polymerase II subunit RPB7: 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
DNA-directed RNA polymerases I, II, and III subunit RPABC4: L
ATP-dependent DNA helicase Q5: P

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

P
U

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase II subunit RPB2

DNA-directed RNA polymerase II subunit RPB3

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

ATP-dependent DNA helicase Q5

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