SMTL ID : 7nw0.1

RNA polymerase II pre-initiation complex with open promoter DNA

Coordinates
PDB Format
Method
ELECTRON MICROSCOPY
Oligo State
hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
Ligands
1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: Unassigned peptide, likely XPB(Non-covalent)
1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
15 x ZN: ZINC ION(Non-covalent)
1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
2 x MG: MAGNESIUM ION(Non-covalent)
1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)
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
RPB1: I
DNA-directed RNA polymerase subunit beta: J
DNA-directed RNA polymerase II subunit RPB3: K
RPOL4c domain-containing protein: L
DNA-directed RNA polymerase II subunit E: M
DNA-directed RNA polymerase II subunit F: N
DNA-directed RNA polymerase II subunit RPB7: O
DNA-directed RNA polymerases I, II, and III subunit RPABC3: P
DNA-directed RNA polymerase II subunit RPB9: Q
DNA-directed RNA polymerases I, II, and III subunit RPABC5: R
RNA_pol_L_2 domain-containing protein: S
RNA polymerase II subunit K: T
Transcription initiation factor IIB: U
TATA-box-binding protein: W
General transcription factor IIF subunit 1: X
General transcription factor IIF subunit 2: Y
Transcription initiation factor IIA subunit 1: 0
Transcription initiation factor IIA subunit 2: 1
General transcription factor IIE subunit 1: 2
Transcription initiation factor IIE subunit beta: 3
Unassigned peptide, likely TFIIE-Beta: 4
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
0
B
1
C
2
D
3
E
4
F
5
G
6
H
7
I
A
J
B
K
C
L
D
M
E
N
F
O
G
P
H
Q
I
R
J
S
K
T
L
U
M
W
O
X
Q
Y
R
0
U
1
V
2
W
3
X
4
Y

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

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

Transcription initiation factor IIB

TATA-box-binding protein

General transcription factor IIF subunit 1

General transcription factor IIF subunit 2

Transcription initiation factor IIA subunit 1

Transcription initiation factor IIA subunit 2

General transcription factor IIE subunit 1

Transcription initiation factor IIE subunit beta

Unassigned peptide, likely TFIIE-Beta

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