8GX9 | pdb_00008gx9

Crystal structure of SARS-CoV-2 RBD with P2C-1F11 and P2B-1G5

• PDB DOI: https://doi.org/10.2210/pdb8GX9/pdb

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


• Deposited: 2022-09-19 Released: 2022-10-12 
• Deposition Author(s): Wang, X., Zhang, L., Ge, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.01 Å
• R-Value Free: 
  0.297 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 antibody P2C-1F11 and RBD

Wang, X., Zhang, L., Ge, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 10-mer - A8B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 231.43 kDa 
• Atom Count: 15,761 
• Modeled Residue Count: 2,082 
• Deposited Residue Count: 2,146 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, B [auth E]	211	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of P2C-1F11	C [auth F], F [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of P2C-1F11	D [auth H], E [auth I]	216	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of P2B-1G5	G [auth M], I [auth N]	214	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of P2B-1G5	H [auth O], J [auth P]	218	Homo sapiens	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.01 Å
• R-Value Free:  0.297 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.511	α = 90
b = 154.856	β = 90
c = 158.423	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Wang, X., Zhang, L., Ge, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171202

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary