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- EMDB-37249: Cryo-EM structure of EBV gH/gL-gp42 in complex with fab 2C1 -

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Basic information

Entry
Database: EMDB / ID: EMD-37249
TitleCryo-EM structure of EBV gH/gL-gp42 in complex with fab 2C1
Map data
Sample
  • Complex: Pentamer complex of gH/gL-gp42 with fab 2C1
    • Protein or peptide: Soluble gp42
    • Protein or peptide: 2C1 heavy chain
    • Protein or peptide: 2C1 light chain
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L
KeywordsHuman gammaherpesvirus 4 / Neutralizing antibody / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell membrane / host cell endosome / carbohydrate binding / host cell Golgi apparatus / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Gammaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain ...Gammaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
BKRF2 / BXLF2 / Glycoprotein 42
Similarity search - Component
Biological speciesEpstein-Barr virus (strain GD1) (Epstein-Barr virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsFang XY / Zhao GX / Zeng MS / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Cell Rep Med / Year: 2024
Title: Potent human monoclonal antibodies targeting Epstein-Barr virus gp42 reveal vulnerable sites for virus infection.
Authors: Ge-Xin Zhao / Xin-Yan Fang / Guo-Long Bu / Shuai-Jia-Bin Chen / Cong Sun / Ting Li / Chu Xie / Yu Wang / Shu-Xin Li / Ning Meng / Guo-Kai Feng / Qian Zhong / Xiang-Wei Kong / Zheng Liu / Mu-Sheng Zeng /
Abstract: Epstein-Barr virus (EBV) is linked to various malignancies and autoimmune diseases, posing a significant global health challenge due to the lack of specific treatments or vaccines. Despite its ...Epstein-Barr virus (EBV) is linked to various malignancies and autoimmune diseases, posing a significant global health challenge due to the lack of specific treatments or vaccines. Despite its crucial role in EBV infection in B cells, the mechanisms of the glycoprotein gp42 remain elusive. In this study, we construct an antibody phage library from 100 EBV-positive individuals, leading to the identification of two human monoclonal antibodies, 2B7 and 2C1. These antibodies effectively neutralize EBV infection in vitro and in vivo while preserving gp42's interaction with the human leukocyte antigen class II (HLA-II) receptor. Structural analysis unveils their distinct binding epitopes on gp42, different from the HLA-II binding site. Furthermore, both 2B7 and 2C1 demonstrate potent neutralization of EBV infection in HLA-II-positive epithelial cells, expanding our understanding of gp42's role. Overall, this study introduces two human anti-gp42 antibodies with potential implications for developing EBV vaccines targeting gp42 epitopes, addressing a critical gap in EBV research.
History
DepositionAug 22, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37249.png

Downloads & links

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Map

FileDownload / File: emd_37249.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 384 pix.
= 328.32 Å		0.86 Å/pix.
x 384 pix.
= 328.32 Å		0.86 Å/pix.
x 384 pix.
= 328.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3103017 - 0.6119628
Average (Standard dev.)-0.00030473294 (±0.010990349)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 328.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37249_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_37249_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 : Pentamer complex of gH/gL-gp42 with fab 2C1

EntireName: Pentamer complex of gH/gL-gp42 with fab 2C1
Components
  • Complex: Pentamer complex of gH/gL-gp42 with fab 2C1
    • Protein or peptide: Soluble gp42
    • Protein or peptide: 2C1 heavy chain
    • Protein or peptide: 2C1 light chain
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L

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Supramolecule #1: Pentamer complex of gH/gL-gp42 with fab 2C1

SupramoleculeName: Pentamer complex of gH/gL-gp42 with fab 2C1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Epstein-Barr virus (strain GD1) (Epstein-Barr virus)

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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: Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Molecular weightTheoretical: 22.398324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GGRVAAAAIT WVPKPNVEVW PVDPPPPVNF NKTAEQEYGD KEVKLPHWTP TLHTFQVPQN YTKANCTYCN TREYTFSYKG CCFYFTKKK HTWNGCFQAC AELYPCTYFY GPTPDILPVV TRNLNAIESL WVGVYRVGEG NWTSLDGGTF KVYQIFGSHC T YVSKFSTV ...String:
GGRVAAAAIT WVPKPNVEVW PVDPPPPVNF NKTAEQEYGD KEVKLPHWTP TLHTFQVPQN YTKANCTYCN TREYTFSYKG CCFYFTKKK HTWNGCFQAC AELYPCTYFY GPTPDILPVV TRNLNAIESL WVGVYRVGEG NWTSLDGGTF KVYQIFGSHC T YVSKFSTV PVSHHECSFL KPCLCVSQRS NSHHHHHH

UniProtKB: Glycoprotein 42

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Macromolecule #2: 2C1 heavy chain

MacromoleculeName: 2C1 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.978212 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLVQSGAEVK KPGSSVKVSC RASGGTFDTY AISWVRQAPG HGLEWMGGII PVSGTANYAQ KFQGRVTITA DESTGTAYMD LSSLRSEDT AVYYCARVPD YGTNTPFDYW GQ

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Macromolecule #3: 2C1 light chain

MacromoleculeName: 2C1 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.849269 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIRLTQSPSS LPASVGDRVT ITCRASQDIA TYLAWYQQKP GRAPNLLIYA TSTLQSGVPP RFSGSRSGTD FTLTISSLQP EDFATYYCQ QLRTYPITFG QGTRLEIK

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Macromolecule #4: Envelope glycoprotein H

MacromoleculeName: Envelope glycoprotein H / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Molecular weightTheoretical: 72.600352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LSEVKLHLDI EGHASHYTIP WTELMAKVPG LSPEALWREA NVTEDLASML NRYKLIYKTS GTLGIALAEP VDIPAVSEGS MQVDASKVH PGVISGLNSP ACMLSAPLEK QLFYYIGTML PNTRPHSYVF YQLRCHLSYV ALSINGDKFQ YTGAMTSKFL M GTYKRVTE ...String:
LSEVKLHLDI EGHASHYTIP WTELMAKVPG LSPEALWREA NVTEDLASML NRYKLIYKTS GTLGIALAEP VDIPAVSEGS MQVDASKVH PGVISGLNSP ACMLSAPLEK QLFYYIGTML PNTRPHSYVF YQLRCHLSYV ALSINGDKFQ YTGAMTSKFL M GTYKRVTE KGDEHVLSLV FGKTKDLPDL RGPFSYPSLT SAQSGDYSLV IVTTFVHYAN FHNYFVPNLK DMFSRAVTMT AA SYARYVL QKLVLLEMKG GCREPELDTE TLTTMFEVSV AFFKVGHAVG ETGNGCVDLR WLAKSFFELT VLKDIIGICY GAT VKGMQS YGLERLAAML MATVKMEELG HLTTEKQEYA LRLATVGYPK AGVYSGLIGG ATSVLLSAYN RHPLFQPLHT VMRE TLFIG SHVVLRELRL NVTTQGPNLA LYQLLSTALC SALEIGEVLR GLALGTESGL FSPCYLSLRF DLTRDKLLSM APQEA TLDQ AAVSNAVDGF LGRLSLERED RDAWHLPAYK CVDRLDKVLM IIPLINVTFI ISSDREVRGS ALYEASTTYL SSSLFL SPV IMNKCSQGAV AGEPRQIPKI QNFTRTQKSC IFCGFALLSY DEKEGLETTT YITSQEVQNS ILSSNYFDFD NLHVHYL LL TTNGTVMEIA GLY

UniProtKB: BXLF2

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Macromolecule #5: Envelope glycoprotein L

MacromoleculeName: Envelope glycoprotein L / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Molecular weightTheoretical: 11.759323 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PCCHVTQLRA QHLLALENIS DIYLVSNQTC DGFSLASLNS PKNGSNQLVI SRCANGLNVV SFFISILKRS SSALTGHLRE LLTTLETLY GSFSVEDLFG ANLNRYAW

UniProtKB: BKRF2

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 227428
FSC plot (resolution estimation)

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