SMTL ID : 7re3.1

SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC dimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-4-2-4-mer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.295, C.301, C.306, C.310 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.295, A:C.301, A:C.306, A:C.310 ZN.2: 5 residues within 4Å: Chain A: C.487, F.571, H.642, C.645, C.646 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.487, A:H.642, A:C.645, A:C.646 ZN.5: 4 residues within 4Å: Chain E: C.9, C.12, C.30, C.33 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.9, E:C.12, E:C.30, E:C.33 ZN.6: 5 residues within 4Å: Chain E: C.54, A.56, C.59, C.76, H.79 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.54, E:C.59, E:C.76, E:H.79 ZN.7: 5 residues within 4Å: Chain E: C.20, A.22, C.23, H.37, H.43 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.20, E:C.23, E:H.37, E:H.43 ZN.12: 5 residues within 4Å: Chain F: C.9, C.12, S.14, C.30, C.33 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.9, F:C.12, F:C.30, F:C.33 ZN.13: 5 residues within 4Å: Chain F: C.54, C.59, V.61, C.76, H.79 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.54, F:C.59, F:C.76, F:H.79 ZN.14: 4 residues within 4Å: Chain F: C.20, C.23, H.37, H.43 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.20, F:C.23, F:H.37, F:H.43 ZN.18: 4 residues within 4Å: Chain J: H.295, C.301, C.306, C.310 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.295, J:C.301, J:C.306, J:C.310 ZN.19: 5 residues within 4Å: Chain J: C.487, F.571, H.642, C.645, C.646 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.487, J:H.642, J:C.645, J:C.646 ZN.22: 4 residues within 4Å: Chain M: C.9, C.12, C.30, C.33 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.9, M:C.12, M:C.30, M:C.33 ZN.23: 5 residues within 4Å: Chain M: C.54, A.56, C.59, C.76, H.79 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.54, M:C.59, M:C.76, M:H.79 ZN.24: 5 residues within 4Å: Chain M: C.20, A.22, C.23, H.37, H.43 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.20, M:C.23, M:H.37, M:H.43 ZN.29: 5 residues within 4Å: Chain N: C.9, C.12, S.14, C.30, C.33 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.9, N:C.12, N:C.30, N:C.33 ZN.30: 5 residues within 4Å: Chain N: C.54, C.59, V.61, C.76, H.79 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.54, N:C.59, N:C.76, N:H.79 ZN.31: 4 residues within 4Å: Chain N: C.20, C.23, H.37, H.43 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.20, N:C.23, N:H.37, N:H.43

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.208, N.209, D.218 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.218 MG.9: 3 residues within 4Å: Chain E: S.293 Ligands: ADP.8, AF3.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.293 MG.16: 4 residues within 4Å: Chain F: G.291, K.292, S.293 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.293 MG.20: 4 residues within 4Å: Chain J: D.208, N.209, D.218 Ligands: ADP.21 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.218 MG.26: 3 residues within 4Å: Chain M: S.293 Ligands: ADP.25, AF3.27 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:S.293 MG.33: 4 residues within 4Å: Chain N: G.291, K.292, S.293 Ligands: ADP.32 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:S.293

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 13 residues within 4Å: Chain A: F.35, K.50, N.52, K.73, H.75, N.79, R.116, D.208, N.209, Y.217, D.218, G.220 Ligands: MG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.52, A:N.209, A:Y.217, A:D.218 Salt bridges: A:K.73, A:K.73, A:R.116 ADP.8: 12 residues within 4Å: Chain E: E.265, P.287, P.288, G.289, T.290, G.291, K.292, S.293, H.294, R.447 Ligands: MG.9, AF3.10 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:E.265, E:E.265, E:P.287, E:G.289, E:T.290, E:T.290, E:G.291, E:K.292, E:S.293, E:S.293, E:H.294, E:H.294 Salt bridges: E:K.292, E:K.324, E:R.447 pi-Cation interactions: E:H.294, E:R.446, E:R.446 ADP.15: 10 residues within 4Å: Chain F: E.265, F.266, G.289, T.290, G.291, K.292, H.294, R.446 Ligands: MG.16, AF3.17 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:E.265, F:G.289, F:T.290, F:G.291, F:K.292, F:S.293 Salt bridges: F:K.292, F:K.324 ADP.21: 13 residues within 4Å: Chain J: F.35, K.50, N.52, K.73, H.75, N.79, R.116, D.208, N.209, Y.217, D.218, G.220 Ligands: MG.20 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:N.52, J:D.208, J:D.218, J:D.218 Salt bridges: J:K.73, J:K.73, J:R.116 ADP.25: 12 residues within 4Å: Chain M: E.265, P.287, P.288, G.289, T.290, G.291, K.292, S.293, H.294, R.447 Ligands: MG.26, AF3.27 14 PLIP interactions: 14 interactions with chain M Hydrogen bonds: M:E.265, M:G.289, M:T.290, M:G.291, M:K.292, M:S.293, M:S.293, M:H.294 Salt bridges: M:K.292, M:K.324, M:R.447 pi-Cation interactions: M:H.294, M:R.446, M:R.446 ADP.32: 10 residues within 4Å: Chain N: E.265, F.266, G.289, T.290, G.291, K.292, H.294, R.446 Ligands: MG.33, AF3.34 8 PLIP interactions: 8 interactions with chain N Hydrogen bonds: N:E.265, N:G.289, N:T.290, N:G.291, N:K.292, N:H.294 Salt bridges: N:K.292, N:K.324

4 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.10: 8 residues within 4Å: Chain E: P.288, K.292, S.293, Q.408, R.447, G.542 Ligands: ADP.8, MG.9 No protein-ligand interaction detected (PLIP) AF3.17: 8 residues within 4Å: Chain F: P.287, P.288, G.289, T.290, G.291, K.292, Q.408 Ligands: ADP.15 No protein-ligand interaction detected (PLIP) AF3.27: 8 residues within 4Å: Chain M: P.288, K.292, S.293, Q.408, R.447, G.542 Ligands: ADP.25, MG.26 No protein-ligand interaction detected (PLIP) AF3.34: 8 residues within 4Å: Chain N: P.287, P.288, G.289, T.290, G.291, K.292, Q.408 Ligands: ADP.32 No protein-ligand interaction detected (PLIP)

2 x 1N7: CHAPSO(Non-covalent)

1N7.11: 6 residues within 4Å: Chain A: V.905 Chain D: A.67 Chain E: L.69, G.71, Y.74, F.94 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: A:V.905, E:F.94, D:A.67 Hydrogen bonds: E:G.71, E:Y.74 1N7.28: 6 residues within 4Å: Chain J: V.905 Chain L: A.67 Chain M: L.69, G.71, Y.74, F.94 6 PLIP interactions: 4 interactions with chain M, 1 interactions with chain J, 1 interactions with chain L Hydrophobic interactions: M:F.94, J:V.905, L:A.67 Hydrogen bonds: M:G.71, M:Y.74, M:Y.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, J. et al., Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex. Nat.Struct.Mol.Biol. (2022)

Release Date

2021-11-24

Peptides

RNA-directed RNA polymerase: AJ
Non-structural protein 8: BDGL
Non-structural protein 7: CK
Helicase: EFMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

J
G

B
B

D
D

G
H

L
J

C
C

K
I

E
E

F
F

M
K

N
L

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7

Helicase

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