SMTL ID : 8p0j.1

Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.415, D.417, D.419 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.415, A:D.415, A:D.417, A:D.417, A:D.419

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: G.42, C.49, T.51, C.52, C.59, G.61, H.62 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.49, A:C.52, A:C.59, A:H.62 ZN.3: 7 residues within 4Å: Chain A: C.90, H.92, C.93, C.130, N.132, C.135, Q.137 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.90, A:C.93, A:C.130, A:C.135 ZN.4: 7 residues within 4Å: Chain B: C.1087, N.1089, C.1090, C.1103, R.1105, C.1106, P.1113 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1087, B:C.1090, B:C.1103, B:C.1106 ZN.5: 7 residues within 4Å: Chain H: C.7, T.9, C.10, K.12, N.37, C.39, C.40 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:C.7, H:T.9, H:C.10, H:C.39, H:C.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grimm, C. et al., Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex (CASP target). To Be Published

Release Date

2024-05-22

Peptides

DNA-directed RNA polymerase 147 kDa polypeptide: A
DNA-directed RNA polymerase 133 kDa polypeptide: B
DNA-directed RNA polymerase 35 kDa subunit: C
DNA-directed RNA polymerase 22 kDa subunit: D
DNA-directed RNA polymerase 19 kDa subunit: E
DNA-directed RNA polymerase 18 kDa subunit: F
Intermediate transcription factor 3 large subunit: G
DNA-directed RNA polymerase 7 kDa subunit: H
mRNA-capping enzyme regulatory subunit OPG124: I
mRNA-capping enzyme catalytic subunit: K
DNA-directed RNA polymerase 30 kDa polypeptide: L
Intermediate transcription factor 3 small subunit: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
G

G
H

H
J

I
L

K
O

L
S

N
I

DNA-directed RNA polymerase 147 kDa polypeptide

DNA-directed RNA polymerase 133 kDa polypeptide

DNA-directed RNA polymerase 35 kDa subunit

DNA-directed RNA polymerase 22 kDa subunit

DNA-directed RNA polymerase 19 kDa subunit

DNA-directed RNA polymerase 18 kDa subunit

Intermediate transcription factor 3 large subunit

DNA-directed RNA polymerase 7 kDa subunit

mRNA-capping enzyme regulatory subunit OPG124

mRNA-capping enzyme catalytic subunit

DNA-directed RNA polymerase 30 kDa polypeptide

Intermediate transcription factor 3 small subunit

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