7FJC

Crystal structure of SARS-CoV-2 Beta RBD complexed with P36-5D2 Fab

• PDB DOI: https://doi.org/10.2210/pdb7FJC/pdb

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


• Deposited: 2021-08-03 Released: 2022-08-10 
• Deposition Author(s): Zhang, L.Q., Wang, X.Q., Shan, S.S., Lan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.269 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Starting Models: experimental

Literature

Crystal structure of SARS-CoV-2 Beta RBD complexed with P36-5D2 Fab

Zhang, L.Q., Wang, X.Q., Shan, S.S., Lan, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68.78 kDa 
• Atom Count: 4,717 
• Modelled Residue Count: 604 
• Deposited Residue Count: 623 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P36-5D2 heavy chain	A [auth H]	222	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P36-5D2 light chain	B [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth E]	187	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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.269 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.11	α = 90
b = 42.113	β = 102.79
c = 122.089	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 

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Zhang, L.Q., Wang, X.Q., Shan, S.S., Lan, J.

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary