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- PDB-9ebc: H5N1 HA in complex with HC-5 Fab -

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Basic information

Entry
Database: PDB / ID: 9ebc
TitleH5N1 HA in complex with HC-5 Fab
Components
  • HC-5 Fab heavy chain
  • HC-5 Fab light chain
  • Hemagglutinin HA1
  • Hemagglutinin HA2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Complex / Viral / Antibody / Monoclonal / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / 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
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsSalas, E. / Liang, B.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To Be Published
Title: H5N1 HA in complex with HC-5 Fab
Authors: Salas, E. / Liang, B.
History
DepositionNov 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data 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
B: Hemagglutinin HA2
G: HC-5 Fab heavy chain
H: HC-5 Fab light chain
C: Hemagglutinin HA1
D: Hemagglutinin HA2
I: HC-5 Fab heavy chain
J: HC-5 Fab light chain
E: Hemagglutinin HA1
F: Hemagglutinin HA2
K: HC-5 Fab heavy chain
L: HC-5 Fab light chain


Theoretical massNumber of molelcules
Total (without water)238,29112
Polymers238,29112
Non-polymers00
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


Mass: 35712.555 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: H5N1 / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: A0AAX6NNG0
#2: Protein Hemagglutinin HA2


Mass: 17491.254 Da / Num. of mol.: 3 / Fragment: UNP residues 345-506
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: H5N1 / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q6DQ18
#3: Antibody HC-5 Fab heavy chain


Mass: 14076.670 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Antibody HC-5 Fab light chain


Mass: 12149.724 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
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: Complex of trimeric HA with three HC-5 Fabs / Type: COMPLEX / Entity ID: #2, #1, #3-#4 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.300 MDa / Experimental value: NO
Source (natural)Organism: Influenza A virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49611 / Symmetry type: POINT
RefinementHighest resolution: 2.87 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01717145
ELECTRON MICROSCOPYf_angle_d1.33623247
ELECTRON MICROSCOPYf_dihedral_angle_d18.8956231
ELECTRON MICROSCOPYf_chiral_restr0.0722493
ELECTRON MICROSCOPYf_plane_restr0.0173000

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