9FMW | pdb_00009fmw

Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6

• PDB DOI: https://doi.org/10.2210/pdb9FMW/pdb
• EM Map EMD-50574: EMDB EMDataResource

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


• Deposited: 2024-06-07 Released: 2025-06-18 
• Deposition Author(s): Bjoernsson, K.H., Walker, M.R., Raghavan, S.S.R., Ward, A.B., Barfod, L.K.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6

Bjoernsson, K.H., Walker, M.R., Raghavan, S.S.R., Ward, A.B., Barfod, L.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A3B2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 452.83 kDa 
• Atom Count: 26,529 
• Modeled Residue Count: 3,382 
• Deposited Residue Count: 4,094 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein,Fibritin	A, B, C	1,277	Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4 This entity is chimeric	Mutation(s): 42  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab of neutralizing mAb K501SP6 heavy chain	D [auth H]	129	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab of neutralizing mAb K501SP6 light chain	E [auth L]	134	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Bjoernsson, K.H., Walker, M.R., Raghavan, S.S.R., Ward, A.B., Barfod, L.K.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	--

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release