SMTL ID : 7oob.1

Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)

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-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: G.63, C.71, T.73, 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: 6 residues within 4Å: Chain A: C.111, F.113, C.114, C.154, C.184, Q.188 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.111, A:C.154, A:C.184 ZN.4: 5 residues within 4Å: Chain B: C.1119, L.1121, 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: 5 residues within 4Å: Chain C: C.88, C.90, F.93, 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: 6 residues within 4Å: Chain I: C.17, C.20, N.22, C.39, C.42, Y.44 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.39, I:C.42 ZN.7: 7 residues within 4Å: Chain I: C.86, K.88, C.89, C.114, A.116, C.119, H.121 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.86, I:C.89, I:C.114, I:C.119 ZN.8: 7 residues within 4Å: Chain J: C.7, T.9, C.10, 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: 6 residues within 4Å: Chain L: C.19, C.22, C.36, E.38, C.39, Y.41 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.19, L:C.22, L:C.36, L:C.39

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: R.460, D.495, D.497, D.499 Chain Q: A.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.499, A:D.499 MG.12: 5 residues within 4Å: Chain M: T.542, D.649, G.923 Ligands: ADP.10, BEF.11 No protein-ligand interaction detected (PLIP)

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

ADP.10: 19 residues within 4Å: Chain M: K.509, L.510, F.511, Q.514, M.537, G.538, L.539, G.540, K.541, T.542, I.543, Q.583, E.587, W.591, N.925, R.953, I.954 Ligands: BEF.11, MG.12 15 PLIP interactions: 15 interactions with chain M Hydrogen bonds: M:K.509, M:F.511, M:Q.514, M:G.538, M:G.540, M:K.541, M:T.542, M:T.542, M:Q.583, M:E.587, M:N.925 Salt bridges: M:K.541, M:R.953, M:R.953 pi-Stacking: M:W.591

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

BEF.11: 10 residues within 4Å: Chain M: M.537, G.538, K.541, E.650, G.678, G.923, R.950, R.953 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kokic, G. et al., Structural basis of human transcription-DNA repair coupling. Nature (2021)

Release Date

2021-10-13

Peptides

DNA-directed RNA polymerase II subunit RPB1: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase II subunit RPB3: C
RPOL4c domain-containing protein: D
DNA-directed RNA polymerase II subunit E: E
DNA-directed RNA polymerase II subunit F: 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
RNA_pol_L_2 domain-containing protein: K
RNA polymerase II subunit K: L
DNA excision repair protein ERCC-6: M
DNA damage-binding protein 1: N
DNA excision repair protein ERCC-8: R

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
b

N
d

R
a

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

RPOL4c domain-containing protein

DNA-directed RNA polymerase II subunit E

DNA-directed RNA polymerase II subunit F

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

RNA_pol_L_2 domain-containing protein

RNA polymerase II subunit K

DNA excision repair protein ERCC-6

DNA damage-binding protein 1

DNA excision repair protein ERCC-8

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