9MQ1 | pdb_00009mq1

Cryo-EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 20D10


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Human monoclonal antibodies that target clade 2.3.4.4b H5N1 hemagglutinin.

Alzua, G.P.Leon, A.N.Yellin, T.Bhavsar, D.Loganathan, M.Bushfield, K.Brouwer, P.J.M.Rodriguez, A.J.Jeevan, T.Webby, R.Marizzi, C.Han, J.Ward, A.B.Duty, J.A.Krammer, F.

(2025) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-025-66829-y
  • Primary Citation of Related Structures:  
    9MQ1, 9MQ2, 9MQ3

  • PubMed Abstract: 

    The highly pathogenic avian influenza H5N1 virus clade 2.3.4.4b has been spreading globally since 2022, causing mortality and morbidity in domestic and wild birds, as well as in mammals, which underscores its potential to cause a pandemic. Here, we generate a panel of anti-hemagglutinin (HA) human monoclonal antibodies (mAbs) against the H5 protein of clade 2.3.4.4b. To develop human chimeric antibodies, H2L2 Harbor Mice®, which express human immunoglobulin germline genes, were immunized with H5 and N1 recombinant proteins from A/mallard/New York/22-008760-007- original/2022 H5N1 virus. Through hybridoma technology, sixteen fully human mAbs are generated, most of which show cross-reactivity against H5 proteins from different clade 2.3.4.4 virus variants. Fourteen out of the sixteen mAbs neutralize the virus in vitro. The mAbs with the strongest hemagglutination inhibition activity also demonstrate greater neutralizing capacity and show increased protective effects in vivo when administered prophylactically or therapeutically in a murine H5N1 challenge model. Using cryo-electron microscopy, we identify a cross-clonotype conserved motif that bound a hydrophobic groove on the head domain of H5 HA. Akin to mAbs against severe acute respiratory syndrome coronavirus 2 during the coronavirus 2019 pandemic, these mAbs could serve as treatments in case of a widespread H5N1 epidemic or pandemic.


  • Organizational Affiliation
    • Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
20D10 Heavy Chain FabA [auth H]122Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
20D10 Light Chain FabB [auth L]112Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1C [auth B],
E [auth A],
G [auth C]
345Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A8E4ZAK5 (Influenza A virus)
Explore A0A8E4ZAK5 
Go to UniProtKB:  A0A8E4ZAK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8E4ZAK5
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2D [auth b],
F [auth a],
H [auth c]
220Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0AAX6NNL9 (Influenza A virus)
Explore A0AAX6NNL9 
Go to UniProtKB:  A0AAX6NNL9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAX6NNL9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth B]
J [auth B]
K [auth B]
L [auth B]
M [auth A]
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth C],
R [auth C],
S [auth C],
T [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N39019C00051

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-12-31
    Changes: Data collection, Database references