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- PDB-9mqa: Cryo-EM structure of hemagglutinin H5N1 in complex with Fab 310-7D11 -

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Basic information

Entry
Database: PDB / ID: 9mqa
TitleCryo-EM structure of hemagglutinin H5N1 in complex with Fab 310-7D11
Components
  • 310-7D11 Fab Heavy chain
  • 310-7D11 Fab Light chain
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Highly pathogenic avian influenza / hemagglutinin H5N1 / bird flu
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
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsMalla, T.N. / Tsybovsky, Y. / Zhou, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Potently Neutralizing Pan H5 monoclonal antibodies provide protection against HPAI H5N1
Authors: Abu-Shmais, A. / Malla, T. / Tsybovsky, Y. / Zhou, T. / Andrews, S. / Kanekiyo, M.
History
DepositionJan 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 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

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
H: 310-7D11 Fab Heavy chain
I: 310-7D11 Fab Heavy chain
J: 310-7D11 Fab Heavy chain
L: 310-7D11 Fab Light chain
M: 310-7D11 Fab Light chain
N: 310-7D11 Fab Light chain


Theoretical massNumber of molelcules
Total (without water)272,25912
Polymers272,25912
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 chain


Mass: 38590.070 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: A0AAX6NN08
#2: Protein Hemagglutinin HA2 chain


Mass: 26166.805 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: A0A5Q2MJY3
#3: Antibody 310-7D11 Fab Heavy chain


Mass: 13882.533 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#4: Antibody 310-7D11 Fab Light chain


Mass: 12113.605 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / 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 between hemagglutinin H5N1 and Fab 310-7D11 / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.26868 MDa / Experimental value: NO
Source (natural)Organism: Influenza A virus / Strain: H5N1
Source (recombinant)Organism: Homo sapiens (human) / Strain: Expi293F
Buffer solutionpH: 7.4 / Details: 10 mM HEPES, 150 mM NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 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: 1900 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEM4.09image acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
9ISOLDEmodel fitting
11PHENIX1.20.1_4487:model refinement
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
14cryoSPARCclassification
15cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1975843
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1461821 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002715296
ELECTRON MICROSCOPYf_angle_d0.591420753
ELECTRON MICROSCOPYf_chiral_restr0.04452267
ELECTRON MICROSCOPYf_plane_restr0.00552692
ELECTRON MICROSCOPYf_dihedral_angle_d5.29512059

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