SMTL ID : 8xx4.1

ASFV RNAP elongation complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x C- U- A- C- A- C- A- A- A: RNA (5'-R(P*CP*UP*AP*CP*AP*CP*AP*AP*A)-3')(Non-covalent)

C-U-A-C-A-C-A-A-A.1: 24 residues within 4Å: Chain A: R.419, D.457, D.459, G.460, D.461 Chain B: Q.498, K.503, T.552, K.555, R.796, Q.797, K.986, K.994, K.1104 Chain H: T.15, T.16, T.17, G.18, T.19, G.20, T.21, A.22, G.23 Ligands: MG.4 No protein-ligand interaction detected (PLIP)

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.59, C.62, C.69, H.72 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.59, A:C.62, A:C.69, A:H.72 ZN.3: 4 residues within 4Å: Chain A: C.99, C.102, C.134, C.137 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.99, A:C.102, A:C.134, A:C.137 ZN.5: 5 residues within 4Å: Chain B: C.1171, C.1174, C.1189, N.1191, C.1192 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1171, B:C.1174, B:C.1189, B:C.1192 ZN.6: 4 residues within 4Å: Chain F: C.4, C.7, C.24, C.26 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4, F:C.7, F:C.24, F:C.26 ZN.7: 4 residues within 4Å: Chain F: C.73, C.76, C.96, C.98 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.73, F:C.76, F:C.96, F:C.98 ZN.8: 4 residues within 4Å: Chain G: C.7, C.10, C.65, C.66 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.7, G:C.10, G:C.65, G:C.66

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.457, D.459, D.461 Ligands: C-U-A-C-A-C-A-A-A.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.457, A:D.459, A:D.461

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, G. et al., Structural basis of RNA polymerase complexes in African swine fever virus. Nat Commun (2025)

Release Date

2025-01-22

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase RPB3-11 homolog: C
DNA-directed RNA polymerase RPB5 homolog: D
D339L: E
C122R: F
DNA-directed RNA polymerase RPB10 homolog: G
RNA polymerase subunit 6: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
G

G
H

I
E

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase RPB3-11 homolog

DNA-directed RNA polymerase RPB5 homolog

D339L

C122R

DNA-directed RNA polymerase RPB10 homolog

RNA polymerase subunit 6

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