[English] 日本語
Yorodumi
- EMDB-33992: Cryo-EM structure of EBV gHgL-gp42 in complex with mAb 10E4 (loca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33992
TitleCryo-EM structure of EBV gHgL-gp42 in complex with mAb 10E4 (localized refinement)
Map data
Sample
  • Complex: gHgL-gp42 in complex with mAb 10E4
    • Complex: gH,gL
      • Protein or peptide: EBV gH
      • Protein or peptide: EBV gL
    • Complex: 10E4
      • Protein or peptide: 10E4 heavy chain
      • Protein or peptide: 10E4 light chain
KeywordsEBV / Cryo-EM / Glycoprotein / gHgL-gp42 complex / Antibody / VIRAL PROTEIN
Biological speciesHuman gammaherpesvirus 4 (Epstein-Barr virus) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 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

-
Structure visualization

Supplemental images

emd_33992.png

Downloads & links

-
Map

FileDownload / File: emd_33992.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.778 Å
Density
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-1.3689843 - 1.5555816
Average (Standard dev.)0.000054935175 (±0.013067248)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #1

Fileemd_33992_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_33992_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : gHgL-gp42 in complex with mAb 10E4

EntireName: gHgL-gp42 in complex with mAb 10E4
Components
  • Complex: gHgL-gp42 in complex with mAb 10E4
    • Complex: gH,gL
      • Protein or peptide: EBV gH
      • Protein or peptide: EBV gL
    • Complex: 10E4
      • Protein or peptide: 10E4 heavy chain
      • Protein or peptide: 10E4 light chain

-
Supramolecule #1: gHgL-gp42 in complex with mAb 10E4

SupramoleculeName: gHgL-gp42 in complex with mAb 10E4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: gH,gL

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

-
Supramolecule #3: 10E4

SupramoleculeName: 100000 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

-
Macromolecule #1: EBV gH

MacromoleculeName: EBV gH / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human gammaherpesvirus 4 (Epstein-Barr virus)
Molecular weightTheoretical: 22.774117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LSEVKLHLDI EGHASHYTIP WTELMAKVPG LSPEALWREA NVTEDLASML NRYKLIYKTS GTLGIALASA PLEKQLFYYI GTMLPNTRP HSYVFYQLRC HLSYVALSIN GDKFQYTGAM TSKFLMGTYK RVTEKGDEHV LSLVFGKTKD LPDLRGPFSY P SLTSAQSG ...String:
LSEVKLHLDI EGHASHYTIP WTELMAKVPG LSPEALWREA NVTEDLASML NRYKLIYKTS GTLGIALASA PLEKQLFYYI GTMLPNTRP HSYVFYQLRC HLSYVALSIN GDKFQYTGAM TSKFLMGTYK RVTEKGDEHV LSLVFGKTKD LPDLRGPFSY P SLTSAQSG DYSLVIVTTF VHYANFHNYF VPNLKDMFSR AVT

-
Macromolecule #2: EBV gL

MacromoleculeName: EBV gL / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human gammaherpesvirus 4 (Epstein-Barr virus)
Molecular weightTheoretical: 8.623719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LALENISDIY LVSNQTCDGF SLASLNSVIS RCANGLNVVS FFISILKRSS SALTGHLREL LTTLETLYGS FSVEDLFGAN

-
Macromolecule #3: 10E4 heavy chain

MacromoleculeName: 10E4 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 12.273763 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QQVKESGGRL VTPGTPLTLT CTASGFSLST YWMSWVRQAP GKGLEYIGVI GGSGSTYYAS WAKGRFTISK TSTTVDLKIT SPTTEDTAT YFCARDSGAG VRFRFWGPGT LVTVSS

-
Macromolecule #4: 10E4 light chain

MacromoleculeName: 10E4 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 11.917251 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DLVMTQTPAS VEAGVGGTVT INCQASENIG SRLAWYQQKP GQPPKLLIYR ASTLESGVPS RFKGSGSGTE FTLTISDLEC ADAATYYCQ CTYGVSITIN YGNDFGGGTE VVVK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 402382

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more