6ZCZ

Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in ternary complex with EY6A Fab and a nanobody.

• PDB DOI: https://doi.org/10.2210/pdb6ZCZ/pdb

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


• Deposited: 2020-06-12 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: 2.65 Å
• R-Value Free: 0.260 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 87.95 kDa 
• Atom Count: 5,839 
• Modelled Residue Count: 754 
• Deposited Residue Count: 797 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth E]	205	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
Nanobody	B [auth F]	151	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
EY6A heavy chain	C [auth H]	226	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
EY6A light chain	D [auth L]	215	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL	F [auth E], G [auth F], H, I [auth H], J [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	K [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.260 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.867	α = 90
b = 177.867	β = 90
c = 87.715	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
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