6LVN | pdb_00006lvn

Structure of the 2019-nCoV HR2 Domain

• PDB DOI: https://doi.org/10.2210/pdb6LVN/pdb

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


• Deposited: 2020-02-04 Released: 2020-02-26 
• Deposition Author(s): Zhu, Y., Sun, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

Crystal structure of HR2 domain of 2019-nCoV S2 subunit

Zhu, Y., Sun, F.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.05 kDa 
• Atom Count: 1,078 
• Modeled Residue Count: 136 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	A, B, C, D	36	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: 2.47 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.195	α = 90
b = 49.729	β = 90
c = 89.576	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Zhu, Y., Sun, F.

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2020-04-01
  Changes: Source and taxonomy, Structure summary
• Version 1.2: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2021-03-10
  Changes: Structure summary
• Version 1.4: 2023-11-29
  Changes: Data collection, Database references, Refinement description