SMTL ID : 7yed.1

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

Coordinates

PDB Format Compare

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, H.184, V.185, C.186, H.199, H.203 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.183, F:C.186, F:C.186 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, C.186, A.188, H.199, H.203 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.183, H:C.186, H:H.199, H:H.203 ZN.22: 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.23: 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 ZN.24: 4 residues within 4Å: Chain W: C.183, C.186, H.199, H.203 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.183, W:C.186, W:H.199, W:H.203 ZN.25: 4 residues within 4Å: Chain X: C.183, C.186, H.199, H.203 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.183, X:C.186, X:H.199, X:H.203 ZN.26: 4 residues within 4Å: Chain Y: C.183, C.186, H.199, H.203 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.183, Y:C.186, Y:H.199, Y:H.203

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

SAM.4: 20 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, K.615 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:S.482, K:S.482, K:Y.552, K:D.553, 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: D.827, G.829, T.830, G.831, D.850, I.851, R.852, D.871, Y.872, M.889, L.890, S.891, A.894, A.895, K.899, R.956 7 PLIP interactions: 7 interactions with chain K Hydrogen bonds: K:T.830, K:D.850, K:I.851, K:R.852, K:D.871, K:D.871 Salt bridges: K:D.850 SAM.7: 20 residues within 4Å: Chain L: 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, K.615 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:S.482, L:S.482, L:Y.552, L:D.553, L:D.561, L:L.562 Salt bridges: L:H.521, L:D.577, L:D.579 pi-Stacking: L:Y.552 SAM.9: 16 residues within 4Å: Chain L: D.827, G.829, T.830, G.831, D.850, I.851, R.852, D.871, Y.872, M.889, L.890, S.891, A.894, A.895, K.899, R.956 8 PLIP interactions: 8 interactions with chain L Hydrogen bonds: L:T.830, L:T.830, L:D.850, L:I.851, L:R.852, L:D.871, L:D.871 Salt bridges: L:D.850 SAM.10: 16 residues within 4Å: Chain M: D.827, G.829, T.830, G.831, D.850, I.851, R.852, D.871, Y.872, M.889, L.890, S.891, A.894, A.895, K.899, R.956 7 PLIP interactions: 7 interactions with chain M Hydrogen bonds: M:T.830, M:D.850, M:D.850, M:I.851, M:R.852, M:D.871 Salt bridges: M:D.850 SAM.11: 19 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 10 PLIP interactions: 10 interactions with chain M Hydrogen bonds: M:S.482, M:S.482, M:Y.552, M:D.561, M:L.562, M:D.577 Salt bridges: M:H.521, M:D.577, M:D.579 pi-Stacking: M:Y.552 SAM.13: 16 residues within 4Å: Chain N: D.827, G.829, T.830, G.831, D.850, I.851, R.852, D.871, Y.872, M.889, L.890, S.891, A.894, A.895, K.899, R.956 6 PLIP interactions: 6 interactions with chain N Hydrogen bonds: N:T.830, N:D.850, N:I.851, N:R.852, N:D.871 Salt bridges: N:D.850 SAM.14: 20 residues within 4Å: Chain N: S.482, D.486, 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 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:S.482, N:G.516, N:S.518, N:Y.552, N:D.561, N:L.562, N:D.577, N:D.577 Salt bridges: N:H.521, N:D.577, N:D.579 pi-Stacking: N:Y.552 SAM.17: 19 residues within 4Å: Chain O: 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 12 PLIP interactions: 12 interactions with chain O Hydrogen bonds: O:S.482, O:G.516, O:S.518, O:Y.552, O:D.553, O:D.561, O:L.562, O:D.577 Salt bridges: O:H.521, O:D.577, O:D.579 pi-Stacking: O:Y.552 SAM.18: 16 residues within 4Å: Chain O: D.827, G.829, T.830, G.831, D.850, I.851, R.852, D.871, Y.872, M.889, L.890, S.891, A.894, A.895, K.899, R.956 8 PLIP interactions: 8 interactions with chain O Hydrogen bonds: O:T.830, O:T.830, O:D.850, O:I.851, O:R.852, O:D.871, O:D.871 Salt bridges: O:D.850

5 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.6: 15 residues within 4Å: Chain K: Q.64, G.65, V.113, N.117, A.167, A.168, G.169, K.171, Y.195, Y.200, T.228, N.229, H.232, I.234, R.278 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:Q.64, K:Q.64, K:N.117, K:A.167, K:Y.195, K:Y.195, K:T.228, K:T.228, K:N.229 Salt bridges: K:K.171, K:K.190, K:K.190, K:H.223, K:H.232, K:R.278, K:R.278 GTP.8: 15 residues within 4Å: Chain L: Q.64, G.65, V.113, N.117, A.167, A.168, G.169, K.171, Y.195, Y.200, T.228, N.229, H.232, I.234, R.278 16 PLIP interactions: 16 interactions with chain L Hydrogen bonds: L:Q.64, L:Q.64, L:N.117, L:A.167, L:Y.195, L:Y.195, L:T.228, L:T.228, L:N.229 Salt bridges: L:K.171, L:K.190, L:K.190, L:H.223, L:H.232, L:R.278, L:R.278 GTP.12: 15 residues within 4Å: Chain M: Q.64, G.65, V.113, N.117, A.167, A.168, G.169, K.171, Y.195, Y.200, T.228, N.229, H.232, I.234, R.278 16 PLIP interactions: 16 interactions with chain M Hydrogen bonds: M:Q.64, M:Q.64, M:N.117, M:A.167, M:Y.195, M:Y.195, M:T.228, M:T.228, M:N.229 Salt bridges: M:K.171, M:K.190, M:K.190, M:H.223, M:H.232, M:R.278, M:R.278 GTP.15: 15 residues within 4Å: Chain N: Q.64, G.65, V.113, N.117, A.167, A.168, G.169, K.171, Y.195, Y.200, T.228, N.229, H.232, I.234, R.278 17 PLIP interactions: 17 interactions with chain N Hydrogen bonds: N:Q.64, N:Q.64, N:N.117, N:A.167, N:Y.195, N:Y.195, N:Y.200, N:T.228, N:T.228, N:N.229 Salt bridges: N:K.171, N:K.190, N:K.190, N:H.223, N:H.232, N:R.278, N:R.278 GTP.16: 15 residues within 4Å: Chain O: Q.64, G.65, V.113, N.117, A.167, A.168, G.169, K.171, Y.195, Y.200, T.228, N.229, H.232, I.234, R.278 16 PLIP interactions: 16 interactions with chain O Hydrogen bonds: O:Q.64, O:Q.64, O:N.117, O:A.167, O:Y.195, O:Y.195, O:T.228, O:T.228, O:N.229 Salt bridges: O:K.171, O:K.190, O:K.190, O:H.223, O:H.232, O:R.278, O:R.278

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.19: 17 residues within 4Å: Chain P: U.21 Chain R: Q.520, R.523, R.526, S.527, S.587, A.588, C.589, D.590, S.682, T.687, H.691, D.734 Chain S: A.14, A.15 Ligands: MG.20, MG.21 10 PLIP interactions: 10 interactions with chain R Hydrogen bonds: R:S.527, R:S.527, R:A.588, R:C.589, R:D.590, R:D.590, R:S.682, R:D.734 Salt bridges: R:R.523, R:R.523

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.20: 1 residues within 4Å: Ligands: UTP.19 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain P: U.21 Chain R: R.523 Ligands: UTP.19 No protein-ligand interaction detected (PLIP)

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

2023-04-05

Peptides

RNA helicase: ABCDEFGHIJUVWXY
Lambda-2 protein: KLMNO
RNA-directed RNA polymerase: R
Mu-2 protein: T

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

U
a

V
b

W
c

X
d

Y
e

K
H

L
I

M
J

N
K

O
L

R
R

T
U

RNA helicase

Lambda-2 protein

RNA-directed RNA polymerase

Mu-2 protein

Related Entries With Identical Sequence