SMTL ID : 8z9h.1

Cryo-EM structure of Thogoto virus polymerase in a transcription elongation-reception conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

2 x G- C- A- A- A- A- A- C- A: RNA (5'-R(P*GP*CP*AP*AP*AP*AP*AP*CP*A)-3')(Non-covalent)

G-C-A-A-A-A-A-C-A.1: 35 residues within 4Å: Chain B: Y.22, E.117, S.119, K.120, R.122, S.421, D.422, D.423, N.471, S.472, T.485, P.488, A.489, N.493 Chain C: R.43, T.45, K.48, K.49, D.50, H.51, A.52, P.53, Q.54 Chain F: C.7, U.8, G.9, U.10, U.11, U.12, U.13, U.14, G.15, C.16, U.17 Ligands: V9G.3 Protein-ligand interaction information (PLIP) not available G-C-A-A-A-A-A-C-A.2: 27 residues within 4Å: Chain G: R.229, S.268, F.301, G.302, K.306, K.309, Y.326, V.328, D.441, N.442, K.461, K.479, I.480, T.481, S.482, F.483, N.559, P.560 Chain H: V.28, A.29, Y.30, G.31, T.32, R.240, V.354, T.361 Ligands: V9G.4 Protein-ligand interaction information (PLIP) not available

2 x V9G: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-ADENOSINE(Non-covalent)

V9G.3: 9 residues within 4Å: Chain B: V.669, L.670, I.671, Q.672 Chain C: K.42, E.210, R.217 Chain F: U.17 Ligands: G-C-A-A-A-A-A-C-A.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.42, C:K.42 Salt bridges: C:R.217 V9G.4: 11 residues within 4Å: Chain G: K.267, S.268, F.301, G.302, K.305, K.309, I.480 Chain H: K.359 Ligands: G-C-A-A-A-A-A-C-A.2, G-C-A-A-A-A-A-C-A.2, G-C-A-A-A-A-A-C-A.2 6 PLIP interactions: 1 interactions with chain H, 5 interactions with chain G Salt bridges: H:K.359, G:K.305, G:K.309, G:K.309, G:K.309 Hydrogen bonds: G:K.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xue, L. et al., Cryo-EM structures of Thogoto virus polymerase reveal unique RNA transcription and replication mechanisms among orthomyxoviruses. Nat Commun (2024)

Release Date

2024-05-29

Peptides

Polymerase acidic protein: AG
RNA-directed RNA polymerase catalytic subunit: BH
Polymerase basic protein 2: CI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
H

B
B

H
I

C
C

I
J

Polymerase acidic protein

RNA-directed RNA polymerase catalytic subunit

Polymerase basic protein 2

Related Entries With Identical Sequence