7N4M

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2151.

• PDB DOI: https://doi.org/10.2210/pdb7N4M/pdb

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


• Deposited: 2021-06-04 Released: 2021-11-10 
• Deposition Author(s): Sankhala, R.S., Joyce, M.G.
• Funding Organization(s): Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.79 Å
• R-Value Free: 0.317 
• R-Value Work: 0.258 
• R-Value Observed: 0.260 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 70.72 kDa 
• Atom Count: 4,170 
• Modelled Residue Count: 537 
• Deposited Residue Count: 646 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WRAIR-2151 antibody Fab heavy chain	A [auth H]	225	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B [auth A]	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
WRAIR-2151 antibody Fab light chain	C [auth L]	216	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.79 Å
• R-Value Free: 0.317 
• R-Value Work: 0.258 
• R-Value Observed: 0.260 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.913	α = 90
b = 112.913	β = 90
c = 239.508	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-10 
Deposition Author(s): Sankhala, R.S., Joyce, M.G.

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Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	W81XWH-18-2-0040

Revision History  

• Version 1.0: 2021-11-10
  Type: Initial release
  
• Version 1.1: 2021-12-15
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description