9MQD | pdb_00009mqd

Cryo-EM structure of hemagglutinin H5N1 in complex with Fab 310-12D03

PDB DOI: https://doi.org/10.2210/pdb9MQD/pdb
EM Map EMD-48521: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-01-02 Released: 2025-08-13
Deposition Author(s): Malla, T.N., Tsybovsky, Y., Zhou, T.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9MQD

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

Literature

Potently Neutralizing Pan H5 monoclonal antibodies provide protection against HPAI H5N1

Abu-Shmais, A., Malla, T., Tsybovsky, Y., Zhou, T., Andrews, S., Kanekiyo, M.

To be published.

Macromolecule Content

Total Structure Weight: 269.04 kDa
Atom Count: 14,509
Modeled Residue Count: 1,841
Deposited Residue Count: 2,397
Unique protein chains: 4

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E	342	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A8E4ZAK5 (Influenza A virus) Explore A0A8E4ZAK5 Go to UniProtKB: A0A8E4ZAK5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8E4ZAK5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F	227	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A8K1XY81 (Influenza A virus) Explore A0A8K1XY81 Go to UniProtKB: A0A8K1XY81
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8K1XY81
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab 310-12D03	G [auth H], H [auth I], I [auth J]	121	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of Fab 310-12D03	J [auth L], K [auth M], L [auth N]	109	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-08-13
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.