6X45 | pdb_00006x45

SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE)

• PDB DOI: https://doi.org/10.2210/pdb6X45/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Mutation(s): Yes 


• Deposited: 2020-05-22 Released: 2021-11-24 
• Deposition Author(s): Kreitler, D.F., Outlaw, V.K., Gellman, S.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.278 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Engineered peptides potently block entry of SARS-CoV-2 into human airway cells

Outlaw, V.K., Yu, Z., Kreitler, D.F., Bovier, F., Porotto, M., Moscona, A., Gellman, S.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 30.44 kDa 
• Atom Count: 1,984 
• Modeled Residue Count: 261 
• Deposited Residue Count: 285 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	A [auth E], B [auth D], D [auth F]	38	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 10
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	C, E [auth B], F [auth A]	57	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 2
UniProt
Find proteins for A0A6C0RQ44 (Severe acute respiratory syndrome coronavirus 2) Explore A0A6C0RQ44  Go to UniProtKB:  A0A6C0RQ44

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.278 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.13904737

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.543	α = 90
b = 54.458	β = 90
c = 80.119	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Kreitler, D.F., Outlaw, V.K., Gellman, S.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM122263
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI114736

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Database references, Structure summary