6M1V | pdb_00006m1v

Crystal structure of post fusion core of 2019-nCoV S2 subunit

• PDB DOI: https://doi.org/10.2210/pdb6M1V/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-02-26 Released: 2020-06-03 
• Deposition Author(s): Sun, H., Song, H., Wang, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Structural basis of HCoV-19 fusion core and an effective inhibition peptide against virus entry.

Sun, H., Li, Y., Liu, P., Qiao, C., Wang, X., Wu, L., Liu, K., Hu, Y., Su, C., Tan, S., Zou, S., Wu, G., Yan, J., Gao, G.F., Qi, J., Wang, Q.

(2020) Emerg Microbes Infect 9: 1238-1241

• PubMed: 32482145 
• DOI: https://doi.org/10.1080/22221751.2020.1770631
• Primary Citation of Related Structures:  
  6M1V

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Organizational Affiliation: 
• CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People's Republic of China.
NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China.
University of Chinese Academy of Sciences, Beijing, People's Republic of China.
Institute of Physical Science and Information, Anhui University, Hefei, People's Republic of China.
College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China.
Savaid Medical School, University of Chinese Academy of Sciences, Beijing, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 12.69 kDa 
• Atom Count: 823 
• Modeled Residue Count: 91 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2,Spike protein S2	A	119	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.666	α = 90
b = 42.666	β = 90
c = 106.648	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Sun, H., Song, H., Wang, Q.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Advisory, Database references, Source and taxonomy, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description