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- EMDB-73043: Cryo-EM structure of post-fusion EBV gB in complex with AMMO2 fab -

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Basic information

Entry
Database: EMDB / ID: EMD-73043
TitleCryo-EM structure of post-fusion EBV gB in complex with AMMO2 fab
Map dataEBV post-fusion state with AMMO2 fabs
Sample
  • Complex: EBV gB with AMMO2 fab
    • Protein or peptide: AMMO2 fab heavy chain
    • Protein or peptide: AMMO2 fab light chain
    • Protein or peptide: BALF4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsPost-fusion / AMMO2 / fab / VIRAL PROTEIN
Function / homology
Function and homology information


viral envelope / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
: / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological specieshuman gammaherpesvirus 4 (Epstein-Barr virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsChou CW / McCool RS / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2026
Title: Structure and immunogenicity of an engineered soluble prefusion-stabilized EBV gB antigen.
Authors: Ryan S McCool / Cory M Acreman / Abigail E Powell / Sofia I Picucci / Daniel J Stieh / Chia-Wei Chou / Jeremy Huynh / Hannah Caruso / Soyoon Park / Jessica O'Rear / Jui-Lin Chen / Brad A ...Authors: Ryan S McCool / Cory M Acreman / Abigail E Powell / Sofia I Picucci / Daniel J Stieh / Chia-Wei Chou / Jeremy Huynh / Hannah Caruso / Soyoon Park / Jessica O'Rear / Jui-Lin Chen / Brad A Palanski / Patrick O Byrne / Madeline R Sponholtz / Jeongryeol Kim / Julie E Ledgerwood / Payton A-B Weidenbacher / Jason S McLellan /
Abstract: Epstein-Barr virus (EBV), the causative agent of mononucleosis, is linked to over 140,000 annual cancer-related deaths globally and increases the risk of multiple sclerosis by up to 32-fold. As a ...Epstein-Barr virus (EBV), the causative agent of mononucleosis, is linked to over 140,000 annual cancer-related deaths globally and increases the risk of multiple sclerosis by up to 32-fold. As a herpesvirus, EBV establishes lifelong infection, and over 90% of U.S. adults are EBV-seropositive. Despite its significant disease burden, no approved EBV vaccines or therapeutics exist. Among EBV envelope glycoproteins, the fusion protein (gB) is strictly required for epithelial and B cell infection. Here, using a combination of AlphaFold-guided modeling, rational design, and ThermoMPNN-informed optimization, we engineer a stabilized prefusion gB variant, C3-GT. This construct incorporates two inter-protomeric disulfide bonds and three cavity-filling substitutions, resulting in a melting temperature of 54 °C. Cryo-EM analysis of this construct reveals the prefusion structure of EBV gB, providing insights into the structural transitions required to adopt the postfusion conformation. Murine immunizations and depletion studies with human sera suggest a trend toward improved functional immunogenicity of C3-GT compared to postfusion gB. Collectively, these studies define engineering principles to stabilize class III fusion proteins, provide reagents to interrogate the human antibody response to EBV gB, and lay a foundation for further studies to develop EBV gB-based vaccine candidates.
History
DepositionOct 6, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73043.png

Downloads & links

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Map

FileDownload / File: emd_73043.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEBV post-fusion state with AMMO2 fabs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 360 pix.
= 335.88 Å		0.93 Å/pix.
x 360 pix.
= 335.88 Å		0.93 Å/pix.
x 360 pix.
= 335.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.933 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.0020847223 - 2.4213917
Average (Standard dev.)0.0026412504 (±0.041117936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 335.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73043_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_73043_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_73043_half_map_2.map
AnnotationHalf map B
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 gB with AMMO2 fab

EntireName: EBV gB with AMMO2 fab
Components
  • Complex: EBV gB with AMMO2 fab
    • Protein or peptide: AMMO2 fab heavy chain
    • Protein or peptide: AMMO2 fab light chain
    • Protein or peptide: BALF4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: EBV gB with AMMO2 fab

SupramoleculeName: EBV gB with AMMO2 fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus)

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Macromolecule #1: AMMO2 fab heavy chain

MacromoleculeName: AMMO2 fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.393003 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGSSIKV SCKTSGGPFS TYGINWVRQA PGQGLEWMGW IIPVFDTSSF AQRFQDRLSI TADASTSTAY MELRSLRSE DTAVYYCARD RVLGAHGANP LNGHHYGMDV WGQGTTVTVS SAST

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Macromolecule #2: AMMO2 fab light chain

MacromoleculeName: AMMO2 fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.13467 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQITQSPSS VSASVGDRVT ITCRANLGIS DWLAWYQQKP GRAPKLLIYA ASSLESGVPS RFSGSGSGIY FTLTISSLQP EDVATYFCQ QANSFPLSFG GGTRVDIART VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQITQSPSS VSASVGDRVT ITCRANLGIS DWLAWYQQKP GRAPKLLIYA ASSLESGVPS RFSGSGSGIY FTLTISSLQP EDVATYFCQ QANSFPLSFG GGTRVDIART VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #3: BALF4

MacromoleculeName: BALF4 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus)
Molecular weightTheoretical: 81.665492 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTRRRVLSVV VLLAALACRL GAQTPEQPAP PATTVQPTAT RQQTSFPFRV CELSSHGDLF RFSSDIQCPS FGTRENHTEG LLMVFKDNI IPYSFKVRSY TKIVTNILIY NGHRADSVTN RHEEKFSVES YETDQMDTIY QCYNAVKMTK DGLTRVYVDR D GVNITVNL ...String:
MTRRRVLSVV VLLAALACRL GAQTPEQPAP PATTVQPTAT RQQTSFPFRV CELSSHGDLF RFSSDIQCPS FGTRENHTEG LLMVFKDNI IPYSFKVRSY TKIVTNILIY NGHRADSVTN RHEEKFSVES YETDQMDTIY QCYNAVKMTK DGLTRVYVDR D GVNITVNL KPTGGLANGV RRYASQTELY DAPGRVEATY RTRTTVNCLI TDMMAKSNSP FEFFVTTTGQ TVEMSPFYDG KN TETFHER ADSFHVRTNY KIVDYDNRGT NPQGERRAFL DKGTYTLSWK LENRTAYCPL QHWQTFDSTI ATETGKSIHF VTD EGTSSF VTNTTVGIEL PDAFKCIEEQ VNKTMHEKYE AVQDRYTKGQ EAITYFITSG GLLLAWLPLT PRSLATVKNL TELT TPTSS PPSSPSPPAP PAARGSTSAA VLGGSGGNAG NATTPVPPAA PGKSLGTLNN PATVQIQFAY DSLRRQINRM LGDLA RAWC LEQKRQNMVL RELTKINPTT VMSSIYGKAV AAKRLGDVIS VSQCVPVNQA TVTLRKSMRV PGSETMCYSR PLVSFS FIN DTKTYEGQLG TDNEIFLTKK MTEVCQATSQ YYFQSGNEIH VYNDYHHFKT IELDGIATLQ TFISLNTSLI ENIDFAS LE LYSRDEQRAS NVFDLEGIFR EYNFQAQNIA GLRKDLDNAV SNGRNQGGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGR A AASSLEVLFQ GPG

UniProtKB: BALF4

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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 / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm

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Image processing

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

3fvc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 154000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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