8WCG | pdb_00008wcg

Crystal structure of SARS-CoV-1 RBD in complex with nanobody aSR29 and aSR347

• PDB DOI: https://doi.org/10.2210/pdb8WCG/pdb

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


• Deposited: 2023-09-12 Released: 2024-09-18 
• Deposition Author(s): Zeng, W.H., Ma, H., Jin, T.C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of SARS-CoV-1 RBD in complex with nanobody aSR29 and aSR347

Zeng, W.H., Ma, H., Jin, T.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

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

Macromolecule Content 

• Total Structure Weight: 101.33 kDa 
• Atom Count: 7,111 
• Modeled Residue Count: 901 
• Deposited Residue Count: 910 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, C [auth B]	197	Severe acute respiratory syndrome coronavirus	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus) Explore P59594  Go to UniProtKB:  P59594
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P59594-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
aSR29 nanobody	B [auth C], D	127	Vicugna pacos	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
aSR347 nanobody	E [auth b], F [auth E]	131	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	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: 2.60 Å
• R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.852	α = 90
b = 134.679	β = 90
c = 136.688	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
autoPROC	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-18 
Deposition Author(s): Zeng, W.H., Ma, H., Jin, T.C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32100745
National Natural Science Foundation of China (NSFC)	China	82272301

Revision History  

• Version 1.0: 2024-09-18
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary