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- PDB-9cxu: Endo H-treated hemagglutinin A/Hong Kong/1/68 -

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Basic information

Entry
Database: PDB / ID: 9cxu
TitleEndo H-treated hemagglutinin A/Hong Kong/1/68
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain,Green fluorescent protein fusion
KeywordsVIRAL PROTEIN / hemagglutinin / glycoprotein / H3
Function / homology
Function and homology information


bioluminescence / viral budding from plasma membrane / generation of precursor metabolites and energy / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...bioluminescence / viral budding from plasma membrane / generation of precursor metabolites and energy / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsTorrents de la Pena, A. / de Paiva Froes Rocha, R. / Ward, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: To Be Published
Title: Structural and immunological characterization of the H3 influenza hemagglutinin during antigenic drift
Authors: de Paiva Froes Rocha, R. / Torrents de la Pena, A. / Ward, A.B. / de Vries, R.P. / Berndsen, Z.T. / Chakraborty, S.
History
DepositionJul 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain,Green fluorescent protein fusion
D: Hemagglutinin HA2 chain,Green fluorescent protein fusion
F: Hemagglutinin HA2 chain,Green fluorescent protein fusion
C: Hemagglutinin HA1 chain
E: Hemagglutinin HA1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,14618
Polymers283,4916
Non-polymers2,65412
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 38523.496 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q91MA7
#2: Protein Hemagglutinin HA2 chain,Green fluorescent protein fusion


Mass: 55973.602 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2), (gene. exp.) Aequorea victoria (jellyfish)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA, GFP / Production host: Homo sapiens (human) / References: UniProt: Q91MA7, UniProt: P42212
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: hemagglutinin A/Hong Kong/1/68 trimer / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Source (natural)Organism: Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4 / Details: TBS
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
4cryoSPARCCTF correction
7Rosettamodel fitting
9Rosettamodel refinement
13cryoSPARC3D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 332294 / Symmetry type: POINT
Atomic model buildingPDB-ID: 4ZCJ

4zcj


Accession code: 4ZCJ / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.02111769
ELECTRON MICROSCOPYf_angle_d1.72315960
ELECTRON MICROSCOPYf_dihedral_angle_d11.3814332
ELECTRON MICROSCOPYf_chiral_restr0.11782
ELECTRON MICROSCOPYf_plane_restr0.0132082

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