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- EMDB-71592: Negative Stain EM map of EBV glycoprotein gp350 in complex with A... -

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Basic information

Entry
Database: EMDB / ID: EMD-71592
TitleNegative Stain EM map of EBV glycoprotein gp350 in complex with ATX-350-2 FAB
Map data
Sample
  • Complex: EBV glycoprotein gp350 1:1 ATX-350-2 FAB
    • Protein or peptide: Surface Glycoprotein gp350
    • Protein or peptide: Fab ATX-350-2 light chain
    • Protein or peptide: Fab ATX-350-2 heavy chain
KeywordsViral protein / Complex / Antibody / EBV / IMMUNE SYSTEM
Function / homology
Function and homology information


host cell membrane / receptor ligand activity / symbiont entry into host cell / virion membrane
Similarity search - Function
Herpesvirus major outer envelope glycoprotein / : / : / : / : / Herpes virus envelope glycoprotein gp350, N-terminal A domain / Herpesvirus envelope glycoprotein gp350, N-terminal B domain / Herpesvirus envelope glycoprotein gp350 N-terminal C domain / Herpesvirus Envelope glycoprotein GP350 C-terminal
Similarity search - Domain/homology
Envelope glycoprotein GP350
Similarity search - Component
Biological specieshuman gammaherpesvirus 4 (Epstein-Barr virus) / Mus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 7.67 Å
AuthorsLang K / Kher G / Aldridge NT / Pancera M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA285227 United States
CitationJournal: Cell Rep Med / Year: 2026
Title: Transgenic mouse-derived human monoclonal antibodies targeting EBV gp350 and gp42 provide basis for therapeutic development.
Authors: Crystal B Chhan / Kevin Lang / Amelia R Davis / Yu-Hsin Wan / Nicholas T Aldridge / Gargi Kher / Samuel C Scharffenberger / Samantha R Hardy / Roman Iureniev / Natalia V Giltiay / Kristina R ...Authors: Crystal B Chhan / Kevin Lang / Amelia R Davis / Yu-Hsin Wan / Nicholas T Aldridge / Gargi Kher / Samuel C Scharffenberger / Samantha R Hardy / Roman Iureniev / Natalia V Giltiay / Kristina R Edwards / Stefan Radtke / Hans-Peter Kiem / Marie Pancera / Andrew T McGuire /
Abstract: Epstein-Barr virus (EBV) causes infectious mononucleosis and contributes to neurodegenerative disorders and malignancies, particularly in immune-compromised hosts. Transplant patients face high risk ...Epstein-Barr virus (EBV) causes infectious mononucleosis and contributes to neurodegenerative disorders and malignancies, particularly in immune-compromised hosts. Transplant patients face high risk of post-transplant lymphoproliferative disease, a life-threatening EBV-driven lymphoma. There are no EBV-specific vaccines or treatments; however, neutralizing antibodies against EBV glycoproteins may offer utility as therapeutic agents. EBV entry into B cells involves gp350, which binds complement receptors, and gp42, which engages HLA class II to trigger fusion. Most existing monoclonal antibodies (mAbs) against these antigens are non-human, limiting clinical use. Using a transgenic mouse model, we generate two gp350 and eight gp42 genetically human neutralizing mAbs that block receptor binding. Structural analyses reveal extended sites of vulnerability relevant to vaccine development. Delivery of a gp42 mAb protects humanized mice from EBV challenge, while a gp350 mAb provides partial protection. These mAbs highlight the utility of transgenic mice to produce therapeutic mAbs for preventing EBV-driven disease.
History
DepositionJul 3, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71592.png

Downloads & links

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Map

FileDownload / File: emd_71592.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.49 Å/pix.
x 90 pix.
= 404.48 Å		4.49 Å/pix.
x 90 pix.
= 404.48 Å		4.49 Å/pix.
x 90 pix.
= 404.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.49422 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.634
Minimum - Maximum-2.269865 - 16.907025999999998
Average (Standard dev.)0.008661878 (±0.33776635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 404.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71592_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71592_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : EBV glycoprotein gp350 1:1 ATX-350-2 FAB

EntireName: EBV glycoprotein gp350 1:1 ATX-350-2 FAB
Components
  • Complex: EBV glycoprotein gp350 1:1 ATX-350-2 FAB
    • Protein or peptide: Surface Glycoprotein gp350
    • Protein or peptide: Fab ATX-350-2 light chain
    • Protein or peptide: Fab ATX-350-2 heavy chain

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Supramolecule #1: EBV glycoprotein gp350 1:1 ATX-350-2 FAB

SupramoleculeName: EBV glycoprotein gp350 1:1 ATX-350-2 FAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 107 KDa

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Macromolecule #1: Surface Glycoprotein gp350

MacromoleculeName: Surface Glycoprotein gp350 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus) / Strain: B95-8
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEAALLVCQY TIQSLIHLTG EDPGFFNVEI PEFPFYPTCN VCTADVNVTI NFDVGGKKHQ LDLDFGQLTP HTKAVYQPRG AFGGSENATN LFLLELLGAG ELALTMRSKK LPINVTTGEE QQVSLESVDV YFQDVFGTMW CHHAEMQNPV YLIPETVPYI KWDNCNSTNI ...String:
MEAALLVCQY TIQSLIHLTG EDPGFFNVEI PEFPFYPTCN VCTADVNVTI NFDVGGKKHQ LDLDFGQLTP HTKAVYQPRG AFGGSENATN LFLLELLGAG ELALTMRSKK LPINVTTGEE QQVSLESVDV YFQDVFGTMW CHHAEMQNPV YLIPETVPYI KWDNCNSTNI TAVVRAQGLD VTLPLSLPTS AQDSNFSVKT QMLGNEIDIE CIMEDGEISQ VLPGDNKFNI TCSGYESHVP SGGILTSTSP VATPIPGTGY AYSLRLTPRP VSRFLGNNSI LYVFYSGNGP KASGGDYCIQ SNIVFSDEIP ASQDMPTNTT DITYVGDNAT YSVPMVTSED ANSPNVTVTA FWAWPNNTET DFKCKWTLTS GTPSGCENIS GAFASNRTFD ITVSGLGTAP KTLIITRTAT NATTTTHKVI FSKAPESTTT SPTLNTTGFA DPNTTTGLPS STHVPTNLTA PASTGPTVST

UniProtKB: Envelope glycoprotein GP350

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Macromolecule #2: Fab ATX-350-2 light chain

MacromoleculeName: Fab ATX-350-2 light chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHSSALLCCL VLLTGVRAEI VLTQSPGTLS LSPGERATLS CRASQSVSSS YLAWYLQKPG QAPRLLIYGA SSRATGIPDR FSGSGSGTDF TLTINRLEPE DFAVYYCQQY GSSHTFGQGT KLEIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN ...String:
MHSSALLCCL VLLTGVRAEI VLTQSPGTLS LSPGERATLS CRASQSVSSS YLAWYLQKPG QAPRLLIYGA SSRATGIPDR FSGSGSGTDF TLTINRLEPE DFAVYYCQQY GSSHTFGQGT KLEIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN ALQSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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Macromolecule #3: Fab ATX-350-2 heavy chain

MacromoleculeName: Fab ATX-350-2 heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHSSALLCCL VLLTGVRAQI TLKESGPTLV KPTQTLTLTC TFSGFSLNTS RVGVGWIRQP PGKALEWLAL IYWNDDKRYS PSLKSRLTIT KDTSNQVVLT MTNMDPVDTA TYYCAHRYSS RWYWYFDLWG RGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD ...String:
MHSSALLCCL VLLTGVRAQI TLKESGPTLV KPTQTLTLTC TFSGFSLNTS RVGVGWIRQP PGKALEWLAL IYWNDDKRYS PSLKSRLTIT KDTSNQVVLT MTNMDPVDTA TYYCAHRYSS RWYWYFDLWG RGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVE

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.5 / Details: 1x TBS
StainingType: NEGATIVE / Material: Uranyl Formate / Details: 2% Uranyl formate

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Electron microscopy

MicroscopeTFS TALOS L120C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 96000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos L120C / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 13586
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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