8BGG

Cryo-EM structure of SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25 (map 5, focus refinement on RBD, W25 and adjacent NTD)

• PDB DOI: https://doi.org/10.2210/pdb8BGG/pdb
• EM Map EMD-16030: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Vicugna pacos
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-27 Released: 2023-03-08 
• Deposition Author(s): Modhiran, N., Lauer, S., Spahn, C.M.T., Watterson, D., Schwefel, D.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25 (map 5, focus refinement on RBD, W25 and adjacent NTD)

Schwefel, D.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 288.25 kDa 
• Atom Count: 4,688 
• Modelled Residue Count: 567 
• Deposited Residue Count: 2,577 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B], B [auth C]	1,205	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 W25	C [auth Y]	167	Vicugna pacos	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth D]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth B], G [auth B], H [auth B], I [auth B], J [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-08 
Deposition Author(s): Modhiran, N., Lauer, S., Spahn, C.M.T., Watterson, D., Schwefel, D.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SCHW1851/1-2

Revision History  

• Version 1.0: 2023-03-08
  Type: Initial release