SMTL ID : 8ebt.1

XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (Cy5)

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: 10 residues within 4Å: Chain B: L.115, C.116, I.117, 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.338, C.341, C.361, C.364 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.338, E:C.341, E:C.361, E:C.364 ZN.3: 4 residues within 4Å: Chain E: C.353, C.356, C.375, C.378 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.353, E:C.356, E:C.375, E:C.378 ZN.4: 4 residues within 4Å: Chain E: C.284, C.287, C.298, C.301 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.284, E:C.287, E:C.298, E:C.301 ZN.5: 6 residues within 4Å: Chain F: C.263, C.266, S.268, C.277, T.279, C.280 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.263, F:C.266, F:C.277, F:C.280 ZN.6: 6 residues within 4Å: Chain F: C.250, C.252, H.253, F.270, C.271, N.272 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.250, F:C.252, F:H.253, F:C.271 ZN.9: 4 residues within 4Å: Chain J: C.4, C.7, C.25, C.28 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.4, J:C.7, J:C.25, J:C.28

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain I: D.14, T.16, S.20, N.23 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.14, I:T.16 CA.8: 6 residues within 4Å: Chain I: D.50, D.52, E.54, V.55, S.56, E.59 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.52

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

General transcription and DNA repair factor IIH helicase subunit XPB: 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: D
General transcription factor IIH subunit 2: E
General transcription factor IIH subunit 3: F
General transcription factor IIH subunit 5: G
DNA repair protein complementing XP-C cells: 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

General transcription and DNA repair factor IIH helicase subunit XPB

General transcription and DNA repair factor IIH helicase subunit XPD

General transcription factor IIH subunit 1

General transcription factor IIH subunit 4

General transcription factor IIH subunit 2

General transcription factor IIH subunit 3

General transcription factor IIH subunit 5

DNA repair protein complementing XP-C cells

Centrin-2

DNA repair protein complementing XP-A cells