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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9FMW

This is version 1.0 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P0DTC2 P10104
Sequence Annotations Expand
Reference Sequence

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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

Find similar proteins by:

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Bjoernsson, K.H.

Raghavan, S.S.R.

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.