7F7H

SARS-CoV-2 S protein RBD in complex with A8-1 Fab

• PDB DOI: https://doi.org/10.2210/pdb7F7H/pdb

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


• Deposited: 2021-06-29 Released: 2022-06-15 
• Deposition Author(s): Dou, Y., Wang, X., Wang, K., Liu, P., Lu, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.275 
• R-Value Work: 0.205 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

High throughput isolation of potent neutralizing antibodies from convalescent COVID-19 patients.

Dou, Y., Jia, Z., Deng, Y., Lan, J., Liu, H.

To be published.

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 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: 133.11 kDa 
• Atom Count: 9,218 
• Modelled Residue Count: 1,204 
• Deposited Residue Count: 1,224 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of A8-1 Fab	A, D [auth C]	218	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of A8-1 Fab	B, E [auth D]	212	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein S1	C [auth E], F	182	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.275 
• R-Value Work: 0.205 
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.772	α = 90
b = 75.66	β = 92.26
c = 181.544	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-06-15 
Deposition Author(s): Dou, Y., Wang, X., Wang, K., Liu, P., Lu, B.

Revision History  

• Version 1.0: 2022-06-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description