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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: Nat Microbiol / Year: 2025
Title: Cross-neutralizing and potent human monoclonal antibodies against historical and emerging H5Nx influenza viruses.
Authors: Alexandra A Abu-Shmais / Gray Freeman / Adrian Creanga / Matthew J Vukovich / Tek Malla / Grace E Mantus / Geoffrey D Shimberg / Rebecca A Gillespie / Vanessa Guerra Canedo / Bernadeta ...Authors: Alexandra A Abu-Shmais / Gray Freeman / Adrian Creanga / Matthew J Vukovich / Tek Malla / Grace E Mantus / Geoffrey D Shimberg / Rebecca A Gillespie / Vanessa Guerra Canedo / Bernadeta Dadonaite / Megan D Rodgers / Ankita J Chopde / Elizabeth Bardwil-Lugones / Tatsiana Bylund / Amy R Henry / Jesmine Roberts-Torres / Timothy S Johnston / Sarah Smith / Eun Sung Yang / Cheng Cheng / Emma L Walker / Michelle Ravichandran / Ingelise J Gordon / Tejaswi S Dittakavi / Douglas S Reed / Theodore C Pierson / Lesia Dropulic / Jesse D Bloom / Yaroslav Tsybovsky / Eli A Boritz / Daniel C Douek / Tongqing Zhou / Masaru Kanekiyo / Sarah F Andrews /
Abstract: Highly pathogenic avian influenza H5Nx viruses are an emerging threat for global health, especially clade 2.3.4.4b H5N1 virus which causes panzootic infections. Here we describe the isolation and ...Highly pathogenic avian influenza H5Nx viruses are an emerging threat for global health, especially clade 2.3.4.4b H5N1 virus which causes panzootic infections. Here we describe the isolation and characterization of broadly cross-neutralizing monoclonal antibodies (mAbs) against diverse H5Nx viruses from individuals who received a monovalent H5N1 vaccine 15 years ago. By screening over 500 mAbs, we identified 5 mAbs that neutralized the majority of H5 clades including 2.3.4.4b and target three distinct conserved epitopes within the HA globular head. Cryo-electron microscopy structures of these mAbs in complex with HA, deep mutational scanning and neutralization escape studies define the sites of vulnerability of H5 HA. These mAbs mediated stronger prophylactic protection against clade 2.3.4.4b H5N1 infection in mice than the best-in-class mAb targeting the HA stem. Our study identified several highly potent broadly neutralizing H5 mAbs from humans that either alone or in combination provide a pragmatic pandemic preparedness option against the threat of panzootic H5N1 influenza.
History
DepositionJan 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: 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
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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