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- EMDB-33990: Cryo-EM structure of EBV gHgL-gp42 in complex with mAbs 3E8 and 5... -

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Basic information

Entry
Database: EMDB / ID: EMD-33990
TitleCryo-EM structure of EBV gHgL-gp42 in complex with mAbs 3E8 and 5E3 (localized refinement)
Map data
Sample
  • Complex: EBV gHgL-gp42 in complex with mAbs 3E8 and 5E3
    • Complex: gp42
      • Protein or peptide: Soluble gp42
    • Complex: 5E3,3E8
      • Protein or peptide: 5E3 heavy chain
      • Protein or peptide: 3E8 heavy chain
      • Protein or peptide: 5E3 light chain
      • Protein or peptide: 3E8 light chain
KeywordsEBV / Cryo-EM / Glycoprotein / gHgL-gp42 complex / Antibody / VIRAL PROTEIN
Function / homologyC-type lectin-like/link domain superfamily / C-type lectin fold / carbohydrate binding / virion membrane / membrane / Glycoprotein 42
Function and homology information
Biological speciesHuman gammaherpesvirus 4 (Epstein-Barr virus) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsLiu L / Sun H / Jiang Y / Hong J / Zheng Q / Li S / Chen Y / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep Med / Year: 2023
Title: Non-overlapping epitopes on the gHgL-gp42 complex for the rational design of a triple-antibody cocktail against EBV infection.
Authors: Junping Hong / Ling Zhong / Liqin Liu / Qian Wu / Wanlin Zhang / Kaiyun Chen / Dongmei Wei / Hui Sun / Xiang Zhou / Xinyu Zhang / Yin-Feng Kang / Yang Huang / Junyu Chen / Guosong Wang / Yan ...Authors: Junping Hong / Ling Zhong / Liqin Liu / Qian Wu / Wanlin Zhang / Kaiyun Chen / Dongmei Wei / Hui Sun / Xiang Zhou / Xinyu Zhang / Yin-Feng Kang / Yang Huang / Junyu Chen / Guosong Wang / Yan Zhou / Yanhong Chen / Qi-Sheng Feng / Hai Yu / Shaowei Li / Mu-Sheng Zeng / Yi-Xin Zeng / Miao Xu / Qingbing Zheng / Yixin Chen / Xiao Zhang / Ningshao Xia /
Abstract: Epstein-Barr virus (EBV) is closely associated with cancer, multiple sclerosis, and post-acute coronavirus disease 2019 (COVID-19) sequelae. There are currently no approved therapeutics or vaccines ...Epstein-Barr virus (EBV) is closely associated with cancer, multiple sclerosis, and post-acute coronavirus disease 2019 (COVID-19) sequelae. There are currently no approved therapeutics or vaccines against EBV. It is noteworthy that combining multiple EBV glycoproteins can elicit potent neutralizing antibodies (nAbs) against viral infection, suggesting possible synergistic effects. Here, we characterize three nAbs (anti-gp42 5E3, anti-gHgL 6H2, and anti-gHgL 10E4) targeting different glycoproteins of the gHgL-gp42 complex. Two antibody cocktails synergistically neutralize infection in B cells (5E3+6H2+10E4) and epithelial cells (6H2+10E4) in vitro. Moreover, 5E3 alone and the 5E3+6H2+10E4 cocktail confer potent in vivo protection against lethal EBV challenge in humanized mice. The cryo-EM structure of a heptatomic gHgL-gp42 immune complex reveals non-overlapping epitopes of 5E3, 6H2, and 10E4 on the gHgL-gp42 complex. Structural and functional analyses highlight different neutralization mechanisms for each of the three nAbs. In summary, our results provide insight for the rational design of therapeutics or vaccines against EBV infection.
History
DepositionAug 2, 2022-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33990.png

Downloads & links

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Map

FileDownload / File: emd_33990.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 448 pix.
= 348.544 Å		0.78 Å/pix.
x 448 pix.
= 348.544 Å		0.78 Å/pix.
x 448 pix.
= 348.544 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.41890854 - 1.1366401
Average (Standard dev.)0.00023202332 (±0.0096226595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 348.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33990_half_map_1.map
Projections & Slices
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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_33990_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : EBV gHgL-gp42 in complex with mAbs 3E8 and 5E3

EntireName: EBV gHgL-gp42 in complex with mAbs 3E8 and 5E3
Components
  • Complex: EBV gHgL-gp42 in complex with mAbs 3E8 and 5E3
    • Complex: gp42
      • Protein or peptide: Soluble gp42
    • Complex: 5E3,3E8
      • Protein or peptide: 5E3 heavy chain
      • Protein or peptide: 3E8 heavy chain
      • Protein or peptide: 5E3 light chain
      • Protein or peptide: 3E8 light chain

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Supramolecule #1: EBV gHgL-gp42 in complex with mAbs 3E8 and 5E3

SupramoleculeName: EBV gHgL-gp42 in complex with mAbs 3E8 and 5E3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: gp42

SupramoleculeName: gp42 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human gammaherpesvirus 4 (Epstein-Barr virus)

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Supramolecule #3: 5E3,3E8

SupramoleculeName: 5E3,3E8 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Soluble gp42

MacromoleculeName: Soluble gp42 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human gammaherpesvirus 4 (Epstein-Barr virus) / Strain: GD1
Molecular weightTheoretical: 15.593692 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
FQVPQNYTKA NCTYCNTREY TFSYKGCCFY FTKKKHTWNG CFQACAELYP CTYFYGPTPD ILPVVTRNLN AIESLWVGVY RVGEGNWTS LDGGTFKVYQ IFGSHCTYVS KFSTVPVSHH ECSFLKPCLC VSQRSNS

UniProtKB: Glycoprotein 42

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Macromolecule #2: 5E3 heavy chain

MacromoleculeName: 5E3 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 13.153532 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QPVEESGGRL VTPGTPLTLT CTVSGFSLST YAMSWVRQAP GKGLEWIGTI SASDTTYFAN WTKGRFTISK ASTTVDLKIT SPTTEDTAT FFCARFSAYE SNRDYFDTFD PWGPGTLVTV SS

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Macromolecule #3: 3E8 heavy chain

MacromoleculeName: 3E8 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 12.123596 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QPVKESGGRL VTPGTPLTLT CTASGFSLSS YWMSWVRQAR GKGLEWIGTA TAGGSAWYAS WAKGRFTISR TSTTVELRMT SLTTEDTAT YFCARDPPGH SGLWGRGTLV TVSS

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Macromolecule #4: 5E3 light chain

MacromoleculeName: 5E3 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 11.543807 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DVVMTQTPSP VSAAVGGTVT IKCQASQNIY RDLAWYQQNP GQPPKLLIYG ASNLASGVPS RFSGSGSGTE YILTISDLEC ADAATYYCQ CSAYGSGYAA HAFGGGTKVD IK

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Macromolecule #5: 3E8 light chain

MacromoleculeName: 3E8 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 11.834026 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DLVMTQTPAS VEAAVGGTVT IKCQASESIG NALAWYQQKP GQPPKLLIYD TSNLASGVSS RFRGSGSGTQ FTLTISDLEC ADAATYYCQ TYYYSGVTTT YQAFGGGTEV DVK

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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

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 167595
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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