SMTL ID : 7nvx.1

TFIIH in a post-translocated state (with ADP-BeF3)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: Unassigned Peptide, likely XPB(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 7 residues within 4Å: Chain H: R.198, L.199, R.200, Q.266, T.267, V.268, S.269 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:T.267, H:V.268, H:V.268 Hydrogen bonds: H:R.198, H:T.267, H:T.267, H:S.269, H:S.269

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

SF4.2: 8 residues within 4Å: Chain A: C.116, H.118, C.134, C.155, F.157, Y.158, C.190, F.193 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.116, A:C.134, A:C.155, A:C.190

7 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain D: C.6, C.9, C.31, C.34 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.6, D:C.9, D:C.31, D:C.34 ZN.4: 4 residues within 4Å: Chain D: C.26, H.28, C.46, C.49 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.26, D:H.28, D:H.28, D:C.46, D:C.49 ZN.5: 4 residues within 4Å: Chain E: C.268, C.271, C.282, C.285 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.268, E:C.271, E:C.282, E:C.285 ZN.6: 4 residues within 4Å: Chain E: C.255, C.257, H.258, C.276 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.255, E:C.257, E:H.258, E:C.276 ZN.7: 4 residues within 4Å: Chain G: C.345, C.348, C.368, C.371 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.345, G:C.348, G:C.368, G:C.371 ZN.8: 4 residues within 4Å: Chain G: C.360, C.363, C.382, C.385 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.360, G:C.363, G:C.382, G:C.385 ZN.9: 4 residues within 4Å: Chain G: C.291, C.294, C.305, C.308 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.291, G:C.294, G:C.305, G:C.308

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

ADP.10: 17 residues within 4Å: Chain H: V.315, R.317, Q.320, P.341, G.343, A.344, G.345, K.346, S.347, L.348, Q.377, W.381, D.616, P.618, R.645 Ligands: MG.11, BEF.12 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:R.317, H:Q.320, H:Q.320, H:G.343, H:A.344, H:G.345, H:K.346, H:S.347, H:S.347, H:S.347, H:Q.377, H:D.616 Salt bridges: H:K.346, H:R.645, H:R.645 pi-Cation interactions: H:R.317

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 4 residues within 4Å: Chain H: S.347, D.441 Ligands: ADP.10, BEF.12 No protein-ligand interaction detected (PLIP)

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

BEF.12: 9 residues within 4Å: Chain H: C.342, K.346, E.442, A.468, S.614, R.642, R.645 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aibara, S. et al., Structures of mammalian RNA polymerase II pre-initiation complexes. Nature (2021)

Release Date

2021-05-05

Peptides

TFIIH basal transcription factor complex helicase XPD subunit: A
General transcription factor IIH subunit 1: B
General transcription factor IIH subunit 4: C
CDK-activating kinase assembly factor MAT1: D
General transcription factor IIH subunit 3: E
General transcription factor IIH subunit 5: F
General transcription factor IIH subunit 2: G
General transcription and DNA repair factor IIH helicase subunit XPB: H
General transcription factor IIE subunit 1: K
Unassigned Peptide, likely TFIIE-Beta: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
1

C
2

D
3

E
4

F
5

G
6

H
7

K
W

L
Z

TFIIH basal transcription factor complex helicase XPD subunit

General transcription factor IIH subunit 1

General transcription factor IIH subunit 4

CDK-activating kinase assembly factor MAT1

General transcription factor IIH subunit 3

General transcription factor IIH subunit 5

General transcription factor IIH subunit 2

General transcription and DNA repair factor IIH helicase subunit XPB

General transcription factor IIE subunit 1

Unassigned Peptide, likely TFIIE-Beta

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