7BV2 | pdb_00007bv2

The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP)

• PDB DOI: https://doi.org/10.2210/pdb7BV2/pdb
• NAKB: 7BV2
• EM Map EMD-30210: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-04-09 Released: 2020-04-22 
• Deposition Author(s): Yin, W., Mao, C., Luan, X., Shen, D., Shen, Q., Su, H., Wang, X., Zhou, F., Zhao, W., Gao, M., Chang, S., Xie, Y.C., Tian, G., Jiang, H.W., Tao, S.C., Shen, J., Jiang, Y., Jiang, H., Xu, Y., Zhang, S., Zhang, Y., Xu, H.E.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir.

Yin, W., Mao, C., Luan, X., Shen, D.D., Shen, Q., Su, H., Wang, X., Zhou, F., Zhao, W., Gao, M., Chang, S., Xie, Y.C., Tian, G., Jiang, H.W., Tao, S.C., Shen, J., Jiang, Y., Jiang, H., Xu, Y., Zhang, S., Zhang, Y., Xu, H.E.

(2020) Science 368: 1499-1504

• PubMed: 32358203 
• DOI: https://doi.org/10.1126/science.abc1560
• Primary Citation Related Structures: 
  7BV1, 7BV2


• PubMed Abstract: 
  

  The pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global crisis. Replication of SARS-CoV-2 requires the viral RNA-dependent RNA polymerase (RdRp) enzyme, a target of the antiviral drug remdesivir. Here we report the cryo-electron microscopy structure of the SARS-CoV-2 RdRp, both in the apo form at 2.8-angstrom resolution and in complex with a 50-base template-primer RNA and remdesivir at 2.5-angstrom resolution. The complex structure reveals that the partial double-stranded RNA template is inserted into the central channel of the RdRp, where remdesivir is covalently incorporated into the primer strand at the first replicated base pair, and terminates chain elongation. Our structures provide insights into the mechanism of viral RNA replication and a rational template for drug design to combat the viral infection.

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Organizational Affiliation: 
• The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
School of Medicine, Tsinghua University, Haidian District, Beijing 100084, China.
Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.
Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
WuxiBiortus Biosciences Co. Ltd., Jiangyin 214437, China.
Center of Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou 310058, China.
Center of Diagnostic Electron Microscopy, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China.
The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. [e-mail] [e-mail] [e-mail] [e-mail].
Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China. [e-mail] [e-mail] [e-mail] [e-mail].
Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China. [e-mail] [e-mail] [e-mail] [e-mail].
Key Laboratory of Immunity and Inflammatory Diseases of Zhejiang Province, Hangzhou 310058, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 159.19 kDa 
• Atom Count: 8,630 
• Modeled Residue Count: 1,036 
• Deposited Residue Count: 1,300 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A	951	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.7.7.48
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 8	B	207	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	C	92	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Primer	D [auth P]	20	Severe acute respiratory syndrome coronavirus 2

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Templete	E [auth T]	30	Severe acute respiratory syndrome coronavirus 2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F86 (Subject of Investigation/LOI)	K [auth P]	[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate C12 H14 N5 O7 P ZBHOHJWLOOFLMW-LTGWCKQJSA-N
POP	H [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
ZN	F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	I [auth A], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-22 
Deposition Author(s): Yin, W., Mao, C., Luan, X., Shen, D., Shen, Q., Su, H., Wang, X., Zhou, F., Zhao, W., Gao, M., Chang, S., Xie, Y.C., Tian, G., Jiang, H.W., Tao, S.C., Shen, J., Jiang, Y., Jiang, H., Xu, Y., Zhang, S., Zhang, Y., Xu, H.E.

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 2.0: 2020-05-06
  Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 3.0: 2020-05-27
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 3.1: 2020-06-10
  Changes: Structure summary
• Version 3.2: 2020-07-15
  Changes: Database references
• Version 3.3: 2020-10-14
  Changes: Derived calculations, Structure summary
• Version 3.4: 2021-03-10
  Changes: Structure summary
• Version 3.5: 2024-03-27
  Changes: Data collection, Database references, Derived calculations