6ZER

Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with EY6A Fab

• PDB DOI: https://doi.org/10.2210/pdb6ZER/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2020-06-16 Released: 2020-06-24 
• Deposition Author(s): Zhou, D., Zhao, Y., Fry, E.E., Ren, J., Stuart, D.I.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust, CAMS Innovation Fund for Medical Sciences (CIFMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 212.31 kDa 
• Atom Count: 14,647 
• Modelled Residue Count: 1,896 
• Deposited Residue Count: 1,932 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth E], D [auth A], G [auth D]	203	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EY6A heavy chain	B [auth H], E [auth B], H [auth F]	226	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
EY6A light chain	C [auth L], F [auth C], I [auth G]	215	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth E], L [auth A], N [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	K [auth L], M [auth C], O [auth F], P [auth G]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.404	α = 90
b = 166.404	β = 90
c = 270.675	γ = 120

Software Package:

Software Name	Purpose
GDA	data collection
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Zhou, D., Zhao, Y., Fry, E.E., Ren, J., Stuart, D.I.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N00065X/1
Wellcome Trust	United Kingdom	101122/Z/13/Z
CAMS Innovation Fund for Medical Sciences (CIFMS)	China	2018-I2M-2-002

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2020-08-12
  Changes: Database references, Structure summary
• Version 1.3: 2020-10-21
  Changes: Database references
• Version 1.4: 2021-02-10
  Changes: Database references
• Version 1.5: 2021-12-22
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.6: 2024-01-24
  Changes: Data collection, Refinement description