9FGU | pdb_00009fgu

SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement)

• PDB DOI: https://doi.org/10.2210/pdb9FGU/pdb
• EM Map EMD-50428: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4, Homo sapiens
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-05-25 Released: 2024-06-12 
• Deposition Author(s): Berlinguer, M., Chaves-Sanjuan, A., Milazzo, F.M., Minenkova, O., De Santis, R., Bolognesi, M.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structure of scFv76-77 in complex with SARS-CoV-2 Omicron Spike protein

Chaves-Sanjuan, A., Bolognesi, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 163.67 kDa 
• Atom Count: 3,241 
• Modeled Residue Count: 413 
• Deposited Residue Count: 1,479 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein,Fibritin	A [auth C]	1,214	Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4 This entity is chimeric	Mutation(s): 21  Gene Names: S, 2, wac
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104  Go to UniProtKB:  P10104
UniProt Groups	P0DTC2P10104
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv76-77 single chain fragment	B [auth E]	265	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Berlinguer, M., Chaves-Sanjuan, A., Milazzo, F.M., Minenkova, O., De Santis, R., Bolognesi, M.

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Funding Organization	Location	Grant Number
Other private	Italy	--

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary