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- EMDB-74798: Cryo-EM local density map of VRC35 Fab bound to N-linked glycans ... -

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Entry
Database: EMDB / ID: EMD-74798
TitleCryo-EM local density map of VRC35 Fab bound to N-linked glycans on the SARS-CoV-2 LP.8.1.9 spike protein
Map data
Sample
  • Complex: Cryo-EM local density map of VRC35 Fab bound to N-linked glycans on the SARS-CoV-2 LP.8.1.9 spike protein
Keywordscanonical antibodies / cryo-EM / HIV-1 envelope / influenza virus hemagglutinin / SARS-CoV-2 spike / Lassa virus glycoprotein complex / variable multivalency / glycan shield / homotypic assembly / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.76 Å
AuthorsCheng J / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS / Becker JE ...Cheng J / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS / Becker JE / Tsybovsky Y / Li N / Zhang B / Du H / Rubin S / Shapiro L / Pierson TC / Doria-Rose NA / Kwong PD / Zhou T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Adv Sci (Weinh) / Year: 2026
Title: Canonical Antibodies Adopt Distinct Binding Modes to Recognize Viral Glycan Shields.
Authors: Jiaxuan Cheng / Evan M Cale / Amirabbas Maghsoudi / Matthew S Sutton / Nancy S Longo / Rebecca A Gillespie / Lingshu Wang / Ivan Kosik / Sue Chong / Atsuhiro Yasuhara / Tatsiana Bylund / ...Authors: Jiaxuan Cheng / Evan M Cale / Amirabbas Maghsoudi / Matthew S Sutton / Nancy S Longo / Rebecca A Gillespie / Lingshu Wang / Ivan Kosik / Sue Chong / Atsuhiro Yasuhara / Tatsiana Bylund / Arne Schön / Prabhanshu Tripathi / Yaroslav Tsybovsky / Haotian Lei / Nicholas C Morano / Allison B Lupatkin / Abraham J Morton / Zabrina C Lang / Jordan E Becker / Isabella R Frascilla / Myungjin Lee / Ning Li / Cuiping Liu / Ryan S Roark / Chen-Hsiang Shen / I-Ting Teng / David J Van Wazer / Danyi Wang / Lingyuan Wu / Goran Ahlsen / Mike Castro / Haijuan Du / Michael J Ernandes / Tiansheng Li / Bob C Lin / Mark K Louder / Krisha McKee / Jonah S Merriam / Sijy O'Dell / Li Ou / Sergei Pletnev / David Prikryl / Qi Qiu / Sarah Rubin / Mallika Sastry / Stephen D Schmidt / Asif Shajahan / Andrea R Shiakolas / Sanjay Srivatsan / Baoshan Zhang / Qiong Zhou / Mark Connors / Jason G Gall / Yicheng Guo / Rick K Huang / Yaoxing Huang / Richard A Koup / Q Paula Lei / John R Mascola / Reda Rawi / Leonid Serebryannyy / Lawrence Shapiro / Zizhang Sheng / David D Ho / Patrick C Wilson / Jonathan W Yewdell / Theodore C Pierson / Masaru Kanekiyo / Nicole A Doria-Rose / Peter D Kwong / Tongqing Zhou /
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 ...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.
History
DepositionDec 23, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74798.png

Downloads & links

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Map

FileDownload / File: emd_74798.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 425.984 Å		0.83 Å/pix.
x 512 pix.
= 425.984 Å		0.83 Å/pix.
x 512 pix.
= 425.984 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.5458197 - 0.35028708
Average (Standard dev.)-0.0008783819 (±0.0048668436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 425.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_74798_half_map_1.map
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AxesZYX

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Half map: #2

Fileemd_74798_half_map_2.map
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Sample components

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Entire : Cryo-EM local density map of VRC35 Fab bound to N-linked glycans ...

EntireName: Cryo-EM local density map of VRC35 Fab bound to N-linked glycans on the SARS-CoV-2 LP.8.1.9 spike protein
Components
  • Complex: Cryo-EM local density map of VRC35 Fab bound to N-linked glycans on the SARS-CoV-2 LP.8.1.9 spike protein

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Supramolecule #1: Cryo-EM local density map of VRC35 Fab bound to N-linked glycans ...

SupramoleculeName: Cryo-EM local density map of VRC35 Fab bound to N-linked glycans on the SARS-CoV-2 LP.8.1.9 spike protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5jw4

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 56057
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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