SMTL ID : 8ebx.1

XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 9 residues within 4Å: Chain B: L.115, C.116, H.118, C.134, T.138, C.155, F.157, C.190, F.193 5 PLIP interactions: 5 interactions with chain B, pi-Cation interactions: B:H.118 Metal complexes: B:C.116, B:C.134, B:C.155, B:C.190

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain E: C.367, C.370, C.390, C.393 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.367, E:C.370, E:C.390, E:C.393 ZN.3: 4 residues within 4Å: Chain E: C.382, C.385, C.404, C.407 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.382, E:C.385, E:C.404, E:C.407 ZN.4: 4 residues within 4Å: Chain E: C.313, C.316, C.327, C.330 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.313, E:C.316, E:C.327, E:C.330 ZN.5: 6 residues within 4Å: Chain F: C.268, C.271, S.273, C.282, T.284, C.285 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.268, F:C.271, F:C.282, F:C.285 ZN.6: 5 residues within 4Å: Chain F: C.255, C.257, H.258, F.275, C.276 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.255, F:C.257, F:H.258, F:C.276 ZN.9: 4 residues within 4Å: Chain J: C.105, C.108, C.126, C.129 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.105, J:C.108, J:C.126, J:C.129

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain I: D.114, D.116, T.118, K.120, N.125 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.114, I:D.116, I:T.118, I:K.120 CA.8: 7 residues within 4Å: Chain I: D.150, D.152, D.154, E.156, V.157, S.158, E.161 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.152, I:D.154, I:D.154, I:E.156, I:E.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J. et al., Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Nature (2023)

Release Date

2023-04-19

Peptides

TFIIH basal transcription factor complex helicase XPB subunit: A
General transcription and DNA repair factor IIH helicase subunit XPD: B
General transcription factor IIH subunit 1: C
General transcription factor IIH subunit 4, p52: D
General transcription factor IIH subunit 2: E
General transcription factor IIH subunit 3: F
General transcription factor IIH subunit 5: G
Xeroderma pigmentosum, complementation group C, isoform CRA_a: H
Centrin-2: I
DNA repair protein complementing XP-A cells: J

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
J

J
K

TFIIH basal transcription factor complex helicase XPB subunit

General transcription and DNA repair factor IIH helicase subunit XPD

General transcription factor IIH subunit 1

General transcription factor IIH subunit 4, p52

General transcription factor IIH subunit 2

General transcription factor IIH subunit 3

General transcription factor IIH subunit 5

Xeroderma pigmentosum, complementation group C, isoform CRA_a

Centrin-2

DNA repair protein complementing XP-A cells

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