9UMY | pdb_00009umy

Cryo-EM structure of hemagglutinin from the A/California/04/2009 (H1N1) influenza virus with stabilizing mutations

PDB DOI: https://doi.org/10.2210/pdb9UMY/pdb
EM Map EMD-64329: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/California/04/2009(H1N1))
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-04-23 Released: 2026-11-04
Deposition Author(s): Kim, Y.G., Lee, G.Y., Lee, J.O.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.21 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9UMY

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

Literature

Stabilization of the trimeric pre-fusion structures of influenza H1 and H9 hemagglutinins by mutations in the stem helices

Kim, Y.G., Lee, G.Y., Lee, J.O.

To be published.

Macromolecule Content

Total Structure Weight: 169.36 kDa
Atom Count: 11,017
Modeled Residue Count: 1,398
Deposited Residue Count: 1,503
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B, C	501	Influenza A virus (A/California/04/2009(H1N1))	Mutation(s): 5 Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1)) Explore C3W5S1 Go to UniProtKB: C3W5S1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3W5S1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	D [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.21 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release