SMTL ID : 7yev.1

In situ structure of polymerase complex of mammalian reovirus in the pre-elongation state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-15-5-1-1-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain F: C.183, V.185, C.186, S.187, H.199, H.203 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.183, F:C.186, F:H.199 ZN.2: 5 residues within 4Å: Chain G: C.183, V.185, C.186, H.199, H.203 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.183, G:C.186, G:H.199, G:H.203 ZN.3: 5 residues within 4Å: Chain H: C.183, V.185, C.186, H.199, H.203 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.183, H:V.185, H:H.203 ZN.14: 5 residues within 4Å: Chain R: C.183, V.185, C.186, H.199, H.203 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:C.183, R:C.186, R:H.199 ZN.15: 5 residues within 4Å: Chain S: C.183, V.185, C.186, H.199, H.203 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.183, S:C.186, S:H.199, S:H.203 ZN.16: 5 residues within 4Å: Chain T: C.183, V.185, C.186, H.199, H.203 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.183, T:C.186, T:H.199, T:H.203 ZN.17: 4 residues within 4Å: Chain U: C.183, C.186, H.199, H.203 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.183, U:C.186, U:H.199, U:H.203 ZN.18: 4 residues within 4Å: Chain V: C.183, C.186, H.199, H.203 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.183, V:C.186, V:H.199, V:H.203

10 x SAM: S-ADENOSYLMETHIONINE(Covalent)(Non-covalent)

SAM.4: 21 residues within 4Å: Chain K: S.482, Y.514, G.516, A.517, S.518, H.521, P.527, G.551, Y.552, D.553, V.560, D.561, L.562, A.563, D.577, V.578, D.579, V.582, D.583, L.594 Chain L: L.387 13 PLIP interactions: 13 interactions with chain K Hydrophobic interactions: K:D.577 Hydrogen bonds: K:S.482, K:G.516, K:S.518, K:Y.552, K:Y.552, K:D.561, K:L.562, K:D.579 Salt bridges: K:H.521, K:D.577, K:D.579 pi-Stacking: K:Y.552 SAM.5: 16 residues within 4Å: Chain K: G.829, T.830, G.831, D.850, I.851, R.852, D.871, Y.872, L.873, M.889, L.890, S.891, A.894, A.895, R.956 Chain O: D.570 12 PLIP interactions: 1 interactions with chain O, 11 interactions with chain K Hydrogen bonds: O:D.570, K:T.830, K:D.850, K:I.851, K:R.852, K:D.871, K:D.871, K:Y.872, K:L.873, K:M.889 Salt bridges: K:D.850 pi-Stacking: K:Y.872 SAM.6: 17 residues within 4Å: Chain K: D.570 Chain L: D.827, G.829, T.830, G.831, D.850, I.851, R.852, D.871, Y.872, L.873, M.889, L.890, S.891, A.894, A.895, R.956 11 PLIP interactions: 9 interactions with chain L, 2 interactions with chain K Hydrogen bonds: L:G.829, L:D.850, L:I.851, L:R.852, L:D.871, L:D.871, L:Y.872, K:D.570 Salt bridges: L:D.850, K:D.570 pi-Stacking: L:Y.872 SAM.7: 19 residues within 4Å: Chain L: S.482, Y.514, G.516, S.518, H.521, P.527, G.551, Y.552, D.553, V.560, D.561, L.562, A.563, D.577, V.578, D.579, V.582, D.583 Chain M: L.387 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:S.482, L:Y.514, L:S.518, L:Y.552, L:Y.552, L:D.561, L:L.562, L:D.577 Salt bridges: L:H.521, L:D.577, L:D.579 pi-Stacking: L:Y.552, L:Y.552 SAM.8: 17 residues within 4Å: Chain L: D.570 Chain M: D.827, G.829, T.830, G.831, D.850, I.851, R.852, D.871, Y.872, L.873, M.889, L.890, S.891, A.894, A.895, R.956 10 PLIP interactions: 9 interactions with chain M, 1 interactions with chain L Hydrogen bonds: M:T.830, M:D.850, M:I.851, M:R.852, M:D.871, M:D.871, M:Y.872, M:M.889, L:D.570 pi-Stacking: M:Y.872 SAM.9: 20 residues within 4Å: Chain M: S.482, Y.514, G.516, A.517, S.518, H.521, P.527, G.551, Y.552, D.553, V.560, D.561, L.562, A.563, D.577, V.578, D.579, V.582, D.583 Chain N: L.387 9 PLIP interactions: 9 interactions with chain M Hydrogen bonds: M:S.518, M:S.518, M:Y.552, M:Y.552, M:D.561, M:L.562 Salt bridges: M:D.577, M:D.579 pi-Stacking: M:Y.552 SAM.10: 18 residues within 4Å: Chain N: S.482, Y.514, G.516, A.517, S.518, H.521, P.527, G.551, Y.552, D.561, L.562, A.563, D.577, V.578, D.579, V.582, D.583 Chain O: L.387 12 PLIP interactions: 12 interactions with chain N Hydrophobic interactions: N:D.577 Hydrogen bonds: N:S.518, N:Y.552, N:L.562, N:A.563, N:D.577, N:D.579 Salt bridges: N:H.521, N:D.577, N:D.579 pi-Stacking: N:Y.552, N:Y.552 SAM.11: 17 residues within 4Å: Chain M: D.570 Chain N: D.827, G.829, T.830, G.831, P.832, D.850, I.851, R.852, D.871, Y.872, L.873, M.889, L.890, S.891, A.894, A.895 9 PLIP interactions: 8 interactions with chain N, 1 interactions with chain M Hydrogen bonds: N:D.850, N:I.851, N:R.852, N:D.871, N:D.871, N:Y.872, N:M.889, M:D.570 pi-Stacking: N:Y.872 SAM.12: 16 residues within 4Å: Chain N: D.570 Chain O: D.827, G.829, T.830, G.831, D.850, I.851, R.852, D.871, Y.872, L.873, M.889, L.890, S.891, A.894, A.895 8 PLIP interactions: 7 interactions with chain O, 1 interactions with chain N Hydrophobic interactions: O:L.890 Hydrogen bonds: O:G.829, O:I.851, O:R.852, O:D.871, O:Y.872, O:L.873, N:D.570 SAM.13: 17 residues within 4Å: Chain K: L.387 Chain O: Y.514, G.516, A.517, S.518, G.551, Y.552, D.553, D.561, L.562, A.563, D.577, V.578, D.579, V.582, D.583, K.615 12 PLIP interactions: 12 interactions with chain O Hydrogen bonds: O:S.518, O:S.518, O:S.518, O:S.518, O:Y.552, O:D.561, O:D.561, O:L.562, O:D.577, O:D.579 Salt bridges: O:D.579 pi-Stacking: O:Y.552

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bao, K. et al., In situ structures of polymerase complex of mammalian reovirus illuminate RdRp activation and transcription regulation. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2023-03-29

Peptides

RNA helicase: ABCDEFGHIJRSTUV
Lambda-2 protein: KLMNO
RNA-directed RNA polymerase: P
Mu-2 protein: Q

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
A

G
B

H
C

I
D

J
E

R
a

S
b

T
c

U
d

V
e

K
H

L
I

M
J

N
K

O
L

P
R

Q
U

RNA helicase

Lambda-2 protein

RNA-directed RNA polymerase

Mu-2 protein

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