9OM5 | pdb_00009om5

Composite map of six VRC35 Fabs and three MEDI8852 Fabs bound to influenza H3N2 Victoria 2011 hemagglutinin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Canonical Antibodies Adopt Distinct Binding Modes to Recognize Viral Glycan Shields.

Cheng, J.Cale, E.M.Maghsoudi, A.Sutton, M.S.Longo, N.S.Gillespie, R.A.Wang, L.Kosik, I.Chong, S.Yasuhara, A.Bylund, T.Schon, A.Tripathi, P.Tsybovsky, Y.Lei, H.Morano, N.C.Lupatkin, A.B.Morton, A.J.Lang, Z.C.Becker, J.E.Frascilla, I.R.Lee, M.Li, N.Liu, C.Roark, R.S.Shen, C.H.Teng, I.T.Van Wazer, D.J.Wang, D.Wu, L.Ahlsen, G.Castro, M.Du, H.Ernandes, M.J.Li, T.Lin, B.C.Louder, M.K.McKee, K.Merriam, J.S.O'Dell, S.Ou, L.Pletnev, S.Prikryl, D.Qiu, Q.Rubin, S.Sastry, M.Schmidt, S.D.Shajahan, A.Shiakolas, A.R.Srivatsan, S.Zhang, B.Zhou, Q.Connors, M.Gall, J.G.Guo, Y.Huang, R.K.Huang, Y.Koup, R.A.Lei, Q.P.Mascola, J.R.Rawi, R.Serebryannyy, L.Shapiro, L.Sheng, Z.Ho, D.D.Wilson, P.C.Yewdell, J.W.Pierson, T.C.Kanekiyo, M.Doria-Rose, N.A.Kwong, P.D.Zhou, T.

(2026) Adv Sci (Weinh) : e77172-e77172

  • DOI: https://doi.org/10.1002/advs.77172
  • Primary Citation Related Structures: 
    9NPM, 9OM5

  • PubMed Abstract: 

    Viral entry glycoproteins are often shielded from immune recognition by dense N-linked glycans that limit antibody access to protein epitopes. While glycan-reactive antibodies with unusual architectures have been described, how canonical Y-shaped antibodies engage these glycan-rich surfaces remains poorly defined. Here, we characterize two human antibodies, VRC35 and VRC36, isolated from an HIV-1-infected donor, that recognize diverse glycosylated viral glycoproteins. Cryo-electron microscopy structural analyses of these antibodies in complex with viral entry glycoproteins, including HIV-1 envelope, influenza hemagglutinin, SARS-CoV-2 spike, and the Lassa virus glycoprotein complex, reveal adaptive Fab stoichiometries ranging from single-Fab binding to dimeric and higher-order assemblies are mediated by intra- and inter-IgG interactions that depend on local glycan organization. Dense glycan clustering on HIV-1 and influenza glycoproteins supports multivalent Fab assemblies and correlates with neutralization activity, whereas sparse glycan environments on SARS-CoV-2 and Lassa virus favor weak or heterogeneous engagement without neutralization. Structural and mutational analyses further demonstrate that homotypic Fab-Fab interactions stabilize multivalent engagement and contribute to neutralizing activity. Together, these findings define a structural framework in which viral glycan organization constrains antibody valency and engagement, while somatic hypermutation contributes to the acquisition of homotypic Fab-Fab interactions that facilitate multivalent recognition of viral glycan shields.


  • Organizational Affiliation
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.

Macromolecule Content 

  • Total Structure Weight: 637.23 kDa 
  • Atom Count: 42,837 
  • Modeled Residue Count: 5,424 
  • Deposited Residue Count: 5,658 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin
A, C, E
348Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A5P1MU07 (Influenza A virus)
Explore A0A5P1MU07 
Go to UniProtKB:  A0A5P1MU07
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5P1MU07
Glycosylation
Glycosylation Sites: 6
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin
B, D, F
223Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A2P1E3C0 (Influenza A virus)
Explore A0A2P1E3C0 
Go to UniProtKB:  A0A2P1E3C0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2P1E3C0
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
MEDI8852 Fab heavy chain
G, I, K
227Homo sapiensMutation(s): 0 
Entity Groups
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
MEDI8852 Fab light chain
H, J, L
206Homo sapiensMutation(s): 0 
Entity Groups
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC35 Fab heavy chain222Homo sapiensMutation(s): 0 
Entity Groups
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC35 Fab light chain219Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Oligosaccharides

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Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth P],
DA [auth R],
FA [auth T],
GA [auth U],
IA [auth W],
BA [auth P],
DA [auth R],
FA [auth T],
GA [auth U],
IA [auth W],
KA [auth Y],
MA [auth m],
NA [auth n],
PA [auth p],
RA [auth r],
Y [auth M],
Z [auth N]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth O],
CA [auth Q],
EA [auth S],
JA [auth X],
LA [auth Z],
AA [auth O],
CA [auth Q],
EA [auth S],
JA [auth X],
LA [auth Z],
QA [auth q],
SA [auth s]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseHA [auth V],
OA [auth o]
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-27
    Type: Initial release
  • Version 1.1: 2026-09-09
    Changes: Data collection, Database references