SMTL ID : 7k04.1

Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: R.107, V.124, S.126, D.129 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.124, A:D.129 CA.2: 3 residues within 4Å: Chain A: T.153, F.159, D.164 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:F.159

1 x SF4: IRON/SULFUR CLUSTER(Covalent)

SF4.3: 10 residues within 4Å: Chain C: C.115, L.116, H.117, V.120, C.133, C.156, Y.158, C.191, Y.193, F.194 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.115, C:C.115, C:C.133, C:C.156

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain E: C.289, C.292, C.305, C.308 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.289, E:C.292, E:C.305, E:C.308 ZN.5: 4 residues within 4Å: Chain F: C.403, C.406, C.437, C.440 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.403, F:C.406, F:C.437, F:C.440 ZN.6: 4 residues within 4Å: Chain F: C.429, C.432, C.451, C.454 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.429, F:C.432, F:C.451, F:C.454 ZN.7: 4 residues within 4Å: Chain F: C.349, C.352, C.363, C.366 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.349, F:C.352, F:C.363, F:C.366 ZN.8: 4 residues within 4Å: Chain F: C.336, C.338, H.339, C.357 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.336, F:C.338, F:H.339, F:C.357

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Eeuwen, T. et al., Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair. Nat Commun (2021)

Release Date

2021-07-28

Peptides

DNA repair protein RAD33: A
General transcription and DNA repair factor IIH subunit TFB2: B
DNA repair helicase RAD3: C
General transcription and DNA repair factor IIH subunit TFB1: D
General transcription and DNA repair factor IIH subunit TFB4: E
General transcription and DNA repair factor IIH subunit SSL1: F
DNA repair protein RAD4: I
DNA repair helicase RAD25: J
RNA polymerase II transcription factor B subunit 5: K

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
2

C
0

D
1

E
4

F
6

I
A

J
7

K
5

DNA repair protein RAD33

General transcription and DNA repair factor IIH subunit TFB2

DNA repair helicase RAD3

General transcription and DNA repair factor IIH subunit TFB1

General transcription and DNA repair factor IIH subunit TFB4

General transcription and DNA repair factor IIH subunit SSL1

DNA repair protein RAD4

DNA repair helicase RAD25

RNA polymerase II transcription factor B subunit 5

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