6M5I | pdb_00006m5i

Crystal structure of 2019-nCoV nsp7-nsp8c complex

• PDB DOI: https://doi.org/10.2210/pdb6M5I/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-10 Released: 2020-06-17 
• Deposition Author(s): Yan, L.M., Ge, J., Zhao, Y., Lou, Z.Y., Rao, Z.H.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 2019-nCoV nsp7-nsp8c complex

Yan, L.M., Ge, J., Lou, Z.Y., Rao, Z.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.02 kDa 
• Atom Count: 1,547 
• Modeled Residue Count: 196 
• Deposited Residue Count: 280 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 8	A [auth B]	198	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
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 7	B [auth A]	82	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.944	α = 90
b = 69.376	β = 90
c = 101.683	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Yan, L.M., Ge, J., Zhao, Y., Lou, Z.Y., Rao, Z.H.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2017YFC0840302

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary