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- EMDB-70607: Composite map of six VRC35 Fabs and three MEDI8852 Fabs bound to ... -

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Basic information

Entry
Database: EMDB / ID: EMD-70607
TitleComposite map of six VRC35 Fabs and three MEDI8852 Fabs bound to influenza H3N2 Victoria 2011 hemagglutinin
Map data
Sample
  • Complex: Complex of six VRC35 Fabs and three MEDI8852 Fabs bound to influenza H3N2 Victoria 2011 hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: MEDI8852 Fab heavy chain
    • Protein or peptide: MEDI8852 Fab light chain
    • Protein or peptide: VRC35 Fab heavy chain
    • Protein or peptide: VRC35 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose
Keywordsbroadly neutralizing antibody / cryo-EM / hemagglutinin / high mannose / homotypic interactions / influenza A virus / multimeric recognition / N-linked glycan / ANTIVIRAL PROTEIN / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 B / 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 speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCheng J / Cale EM / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS ...Cheng J / Cale EM / 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
DepositionMay 13, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70607.png

Downloads & links

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Map

FileDownload / File: emd_70607.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 420 pix.
= 348.6 Å		0.83 Å/pix.
x 420 pix.
= 348.6 Å		0.83 Å/pix.
x 420 pix.
= 348.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-21.399913999999999 - 38.508290000000002
Average (Standard dev.)0.011505172 (±1.3756088)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 348.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex of six VRC35 Fabs and three MEDI8852 Fabs bound to influe...

EntireName: Complex of six VRC35 Fabs and three MEDI8852 Fabs bound to influenza H3N2 Victoria 2011 hemagglutinin
Components
  • Complex: Complex of six VRC35 Fabs and three MEDI8852 Fabs bound to influenza H3N2 Victoria 2011 hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: MEDI8852 Fab heavy chain
    • Protein or peptide: MEDI8852 Fab light chain
    • Protein or peptide: VRC35 Fab heavy chain
    • Protein or peptide: VRC35 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: Complex of six VRC35 Fabs and three MEDI8852 Fabs bound to influe...

SupramoleculeName: Complex of six VRC35 Fabs and three MEDI8852 Fabs bound to influenza H3N2 Victoria 2011 hemagglutinin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 38.937195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSHI LCLVFAQKLP GNDNSTATLC LGHHAVPNGT IVKTICNDQI EVTNATELVQ NSSIGEICDS PHQILDGENC TLIDALLGD PQCDGFQNKK WDLFVERSKA YSNCYPYDVP DYASLRSLVA SSGTLEFNNE SFNWTGVTQN GTSSACIRRS N NSFFSRLN ...String:
MKTIIALSHI LCLVFAQKLP GNDNSTATLC LGHHAVPNGT IVKTICNDQI EVTNATELVQ NSSIGEICDS PHQILDGENC TLIDALLGD PQCDGFQNKK WDLFVERSKA YSNCYPYDVP DYASLRSLVA SSGTLEFNNE SFNWTGVTQN GTSSACIRRS N NSFFSRLN WLTHLNFKYP ALNVTMPNNE QFDKLYIWGV HHPGTDKDQI FLYAQSSGRI TVSTKRSQQA VIPNIGSRPR IR NIPSRIS IYWTIVKPGD ILLINSTGNL IAPRGYFKIR SGKSSIMRSD APIGKCNSEC ITPNGSIPND KPFQNVNRIT YGA CPRYVK QSTLKLATGM RNVPEKQRRR RR

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 25.410279 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RGIFGAIAGF IENGWEGMVD GWYGFRHQNS EGRGQAADLK STQAAIDCIN GKLNRLIGKT NEKFHQIEKE FSEVEGRIQD LEKYVEDTK IDLWSYNAEL LVALENQHTI DLTDSEMNKL FEKTKKQLRE NAEDMGNGCF KIYHKCDNAC IGSIRNGTYD H DVYRDEAL ...String:
RGIFGAIAGF IENGWEGMVD GWYGFRHQNS EGRGQAADLK STQAAIDCIN GKLNRLIGKT NEKFHQIEKE FSEVEGRIQD LEKYVEDTK IDLWSYNAEL LVALENQHTI DLTDSEMNKL FEKTKKQLRE NAEDMGNGCF KIYHKCDNAC IGSIRNGTYD H DVYRDEAL NNRFQIKGVS GLEVLFQGPG SGYIPEAPRD GQAYVRKDGE WVLLSTFLGH HHHHH

UniProtKB: Hemagglutinin

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Macromolecule #3: MEDI8852 Fab heavy chain

MacromoleculeName: MEDI8852 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.413189 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQSGPG LVKPSQTLSL TCAISGDSVS SYNAVWNWIR QSPSRGLEWL GRTYYRSGWY NDYAESVKSR ITINPDTSKN QFSLQLNSV TPEDTAVYYC ARSGHITVFG VNVDAFDMWG QGTMVTVSSA STKGPSVFPL APSSKSTSGT AALGCLVKDY F PEPVTVSW ...String:
QVQLQQSGPG LVKPSQTLSL TCAISGDSVS SYNAVWNWIR QSPSRGLEWL GRTYYRSGWY NDYAESVKSR ITINPDTSKN QFSLQLNSV TPEDTAVYYC ARSGHITVFG VNVDAFDMWG QGTMVTVSSA STKGPSVFPL APSSKSTSGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEP

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Macromolecule #4: MEDI8852 Fab light chain

MacromoleculeName: MEDI8852 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.450832 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTQSPSSLSA SVGDRVTITC RTSQSLSSYT HWYQQKPGKA PKLLIYAASS RGSGVPSRFS GSGSGTDFTL TISSLQPEDF ATYYCQQSR TFGQGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS GNSQESVTEQ D SKDSTYSL ...String:
MTQSPSSLSA SVGDRVTITC RTSQSLSSYT HWYQQKPGKA PKLLIYAASS RGSGVPSRFS GSGSGTDFTL TISSLQPEDF ATYYCQQSR TFGQGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS GNSQESVTEQ D SKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGE

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Macromolecule #5: VRC35 Fab heavy chain

MacromoleculeName: VRC35 Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.90907 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLRQWGAG LVKPGETLSV TCELYGDSLR DFYWTWVRQA PGKPLQWVGE INVALNYKYN PSVRMTISVD EPKNQFTLKI FYTTAADTA TYFCARGRGT VATELAMWGP GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
QVQLRQWGAG LVKPGETLSV TCELYGDSLR DFYWTWVRQA PGKPLQWVGE INVALNYKYN PSVRMTISVD EPKNQFTLKI FYTTAADTA TYFCARGRGT VATELAMWGP GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDK

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Macromolecule #6: VRC35 Fab light chain

MacromoleculeName: VRC35 Fab light chain / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.033865 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NIVLTQTALS APVVLGQPAS ISCRSSETLH HSDGRTYLSW LHQGRGQPPR LLLYHISQRS FGVSDRISGR GAGTNFTLDI SKVEPEDAG LYYCMQATQF PRTFGPGTVL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
NIVLTQTALS APVVLGQPAS ISCRSSETLH HSDGRTYLSW LHQGRGQPPR LLLYHISQRS FGVSDRISGR GAGTNFTLDI SKVEPEDAG LYYCMQATQF PRTFGPGTVL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #11: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 11 / Number of copies: 2 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1780000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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