9NPM | pdb_00009npm

Composite map of three pairs of dimeric VRC36 Fabs bound to HIV-1 BG505.T332N DS-SOSIP.664 Env trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9NPM

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: 528.98 kDa 
  • Atom Count: 35,931 
  • Modeled Residue Count: 4,362 
  • Deposited Residue Count: 4,500 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp120A [auth C],
G [auth E],
M [auth A]
473Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 16
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp41B [auth D],
H [auth F],
N [auth B]
153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1)
Explore Q2N0S5 
Go to UniProtKB:  Q2N0S5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC36 Fab heavy chain223Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC36 Fab light chain214Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
DA [auth d],
EA [auth e],
GA [auth g],
HA [auth h],
OA [auth o],
DA [auth d],
EA [auth e],
GA [auth g],
HA [auth h],
OA [auth o],
PA [auth p],
RA [auth r],
S,
SA [auth s],
T,
V,
W
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 6
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-glucopyranoseFA [auth f],
QA [auth q],
U
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-glucopyranoseIA [auth i],
TA [auth t],
X
9N-Glycosylation
Glycosylation Resources
GlyTouCan: G63337SS
GlyCosmos: G63337SS
GlyGen: G63337SS
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-glucopyranoseJA [auth j],
KA [auth k],
VA [auth v],
Y,
Z
8N-Glycosylation
Glycosylation Resources
GlyTouCan: G83582BK
GlyCosmos: G83582BK
GlyGen: G83582BK
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-glucopyranose
AA [auth a],
BA [auth b],
LA [auth l],
MA [auth m],
WA [auth w],
AA [auth a],
BA [auth b],
LA [auth l],
MA [auth m],
WA [auth w],
XA [auth x]
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G09724ZC
GlyCosmos: G09724ZC
GlyGen: G09724ZC
Entity ID: 10
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-glucopyranoseCA [auth c],
NA [auth n],
ZA [auth z]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 11
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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-glucopyranoseUA [auth u]6N-Glycosylation
Glycosylation Resources
GlyTouCan: G01760ZU
GlyCosmos: G01760ZU
GlyGen: G01760ZU
Entity ID: 12
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranoseYA [auth y]2N/A
Glycosylation Resources
GlyTouCan: G00891MP
GlyCosmos: G00891MP
GlyGen: G00891MP

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
AB [auth C]
BB [auth C]
CB [auth C]
DB [auth C]
EB [auth C]
AB [auth C],
BB [auth C],
CB [auth C],
DB [auth C],
EB [auth C],
FB [auth E],
GB [auth E],
HB [auth E],
IB [auth E],
JB [auth E],
KB [auth A],
LB [auth A],
MB [auth A],
NB [auth A],
OB [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 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: 2026-08-19
    Type: Initial release
  • Version 1.1: 2026-09-09
    Changes: Data collection, Database references