8XRQ

SARS-CoV-2 BA.1 spike RBD in complex bound with VacBB-639

• PDB DOI: https://doi.org/10.2210/pdb8XRQ/pdb
• EM Map EMD-38610: EMDB EMDataResource

• Classification: PROTEIN BINDING
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-01-08 Released: 2024-12-18 
• Deposition Author(s): Liu, C.C., Ju, B., Zhang, Z.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structure of SARS-COV-2 Spike RBD and VacBB-551 complex at 2.7 Angstroms resolution.

Liu, C.C., Ju, B., Zhang, Z.

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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 50.41 kDa 
• Atom Count: 3,210 
• Modelled Residue Count: 407 
• Deposited Residue Count: 452 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	223	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 15  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
Heavy chain of VacBB 639 Fab	B	122	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of VacBB 639 Fab	C	107	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.2
MODEL REFINEMENT	PHENIX	1.20

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Liu, C.C., Ju, B., Zhang, Z.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	82025022

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release