8H91 | pdb_00008h91

Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with nanobody N19

• PDB DOI: https://doi.org/10.2210/pdb8H91/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Vicugna pacos
• Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-10-24 Released: 2023-11-01 
• Deposition Author(s): Zhang, Y.T., Li, J., Zhang, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.07 Å
• R-Value Free: 
  0.284 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with nanobody N19

Zhang, Y.T., Li, J., Zhang, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 68.68 kDa 
• Atom Count: 4,728 
• Modeled Residue Count: 621 
• Deposited Residue Count: 622 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, B	194	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
nanobody	C, D	117	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.07 Å
• R-Value Free:  0.284 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.366	α = 90
b = 57.366	β = 90
c = 444.072	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-01 
Deposition Author(s): Zhang, Y.T., Li, J., Zhang, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-11-01
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description