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- EMDB-60928: Cryo-EM structure of EBV gH/gL/gp42 in complex with fab 4G12 -

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Basic information

Entry
Database: EMDB / ID: EMD-60928
TitleCryo-EM structure of EBV gH/gL/gp42 in complex with fab 4G12
Map data
Sample
  • Complex: gH/gL/gp42 in complex with fab 4G12
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L
    • Protein or peptide: Soluble gp42
    • Protein or peptide: 4G12 fab H chain
    • Protein or peptide: 4G12 fab L chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endosome membrane / carbohydrate binding / host cell Golgi apparatus / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
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
Glycoprotein 42 / Envelope glycoprotein H / Envelope glycoprotein L
Similarity search - Component
Biological speciesHuman gammaherpesvirus 8 / human gammaherpesvirus 4 (Epstein-Barr virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsFang XY / Zhao GX / Liu Z / Zeng MS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: To Be Published
Title: Structure of KSHV glycoprotein B
Authors: Fang XY / Zhao GX / Liu Z / Zeng MS
History
DepositionJul 23, 2024-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60928.png

Downloads & links

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Map

FileDownload / File: emd_60928.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.51 Å/pix.
x 512 pix.
= 261.12 Å		0.51 Å/pix.
x 512 pix.
= 261.12 Å		0.51 Å/pix.
x 512 pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.51 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.30597043 - 0.429287
Average (Standard dev.)0.00051654654 (±0.011426469)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60928_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_60928_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 : gH/gL/gp42 in complex with fab 4G12

EntireName: gH/gL/gp42 in complex with fab 4G12
Components
  • Complex: gH/gL/gp42 in complex with fab 4G12
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L
    • Protein or peptide: Soluble gp42
    • Protein or peptide: 4G12 fab H chain
    • Protein or peptide: 4G12 fab L chain

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Supramolecule #1: gH/gL/gp42 in complex with fab 4G12

SupramoleculeName: gH/gL/gp42 in complex with fab 4G12 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human gammaherpesvirus 8

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Macromolecule #1: Envelope glycoprotein H

MacromoleculeName: Envelope glycoprotein H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus)
Molecular weightTheoretical: 73.130984 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 KGDEHVLSLI 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 MLDQ AAVSNAVDGF LGRLSLERED RDAWHLPAYK CVDRLDKVLM IIPLINVTFI ISSDREVRGS ALYEASTTYL SSSLFL SPV IMNKCSQGAV AGEPRQIPKI QNFTRTQKSC IFCGFALLSY DEKEGLETTT YITSQEVQNS ILSSNYFDFD NLHVHYL LL TTNGTVMEIA GLYEERA

UniProtKB: Envelope glycoprotein H

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Macromolecule #2: Envelope glycoprotein L

MacromoleculeName: Envelope glycoprotein L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus)
Molecular weightTheoretical: 12.491126 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
WAYPCCHVTQ LRAQHLLALE NISDIYLVSN QTCDGFSLAS LNSPKNGSNQ LVISRCANGL NVVSFFISIL KRSSSALTSH LRELLTTLE SLYGSFSVED LFGANLNRYA WHR

UniProtKB: Envelope glycoprotein L

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Macromolecule #3: Soluble gp42

MacromoleculeName: Soluble gp42 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (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 #4: 4G12 fab H chain

MacromoleculeName: 4G12 fab H chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.144529 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGQSLRI SCQGSGHSFA DYWINWVRQK PGEGLEWMGR VDPSDSHATY SPSFRGHVTF STDKSISTAY LQWSSLRAS DTAMYFCARS YYDSRTGSVS PYYFDYWGQG TLVTVSS

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Macromolecule #5: 4G12 fab L chain

MacromoleculeName: 4G12 fab L chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.614699 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLIQPRSV SGSPGQSVTI SCTGTSTDVG NYNYVSWYQQ HPGTAPRFLI YDVSNRPSGV PDRFSGSKSG NTASLTISGL QADDEADYY CCSYAGKSIV VCGGGTQLTV LG

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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: 8.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73125
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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