7C01

Molecular basis for a potent human neutralizing antibody targeting SARS-CoV-2 RBD

• PDB DOI: https://doi.org/10.2210/pdb7C01/pdb

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


• Deposited: 2020-04-29 Released: 2020-05-27 
• Deposition Author(s): Shi, R., Qi, J., Wang, Q., Gao, F.G., Yan, J.
• Funding Organization(s): Chinese Academy of Sciences, Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 0.265 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 149.68 kDa 
• Atom Count: 9,670 
• Modelled Residue Count: 1,256 
• Deposited Residue Count: 1,358 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, D [auth B]	229	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
CB6 heavy chain	B [auth H], E [auth C]	233	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CB6 light chain	C [auth L], F [auth D]	217	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 0.265 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.4	α = 90
b = 106.73	β = 90
c = 170.59	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
HKL-2000	data reduction
UCSD-system	data processing
PHASER	phasing
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Shi, R., Qi, J., Wang, Q., Gao, F.G., Yan, J.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB29040201
Ministry of Science and Technology (MoST, China)	China	2018ZX09711003
Ministry of Science and Technology (MoST, China)	China	2020YFC0841400
National Natural Science Foundation of China (NSFC)	China	81922044

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-06-10
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2020-08-19
  Changes: Database references, Structure summary
• Version 1.4: 2021-03-10
  Changes: Structure summary
• Version 1.5: 2023-11-29
  Changes: Data collection, Database references, Refinement description