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- EMDB-71589: Negative stain EM map of EBV glycoprotein gH/gL in complex with g... -

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Basic information

Entry
Database: EMDB / ID: EMD-71589
TitleNegative stain EM map of EBV glycoprotein gH/gL in complex with glycoprotein gp42 and HLA-DR1 Beta chain
Map data
Sample
  • Complex: Co-expressed EBV glycoprotein gHgL Complex 1:1 with gp42, then complex 1:1 with HLA-DR1 BETA CHAIN
    • Protein or peptide: Surface Glycoprotein gH
    • Protein or peptide: Surface Glycoprotein gL
    • Protein or peptide: Surface Glycoprotein gp42
    • Protein or peptide: HLA class II histocompatibility antigen, DRB1 beta chain
KeywordsViral Protein / Complex. Antibody / EBV / IMMUNE SYSTEM
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of kinase activity ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of kinase activity / positive regulation of memory T cell differentiation / positive regulation of T cell mediated immune response to tumor cell / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / CD4 receptor binding / intermediate filament / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / host cell membrane / epidermis development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / MHC class II antigen presentation / host cell endosome membrane / trans-Golgi network membrane / protein tetramerization / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / positive regulation of T cell activation / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / Interferon gamma signaling / positive regulation of protein phosphorylation / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / carbohydrate binding / host cell Golgi apparatus / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / immune response / Golgi membrane / fusion of virus membrane with host plasma membrane / lysosomal membrane / external side of plasma membrane / viral envelope / symbiont entry into host cell / positive regulation of DNA-templated transcription / host cell plasma membrane / virion membrane / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma 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 / MHC class II, beta chain, N-terminal ...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 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha/beta chain, N-terminal / C-type lectin-like/link domain superfamily / C-type lectin fold / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DRB1 beta chain / Glycoprotein 42 / Envelope glycoprotein L / Envelope glycoprotein H
Similarity search - Component
Biological specieshuman gammaherpesvirus 4 (Epstein-Barr virus) / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 11.62 Å
AuthorsLang K / Duy M / Pancera M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA285227 United States
CitationJournal: To Be Published
Title: Genetically protective human EBV-neutralizing mAbs targeting multiple receptor-binding sites mAbs elicited in transgenic mice
Authors: Chan CB / Lang K / Davis AR / Wan YH / Aldridge NT / Kher G / Scharffenberger SC / Hardy SR / Iureniev R / Giltiay NV / Edwards KR / Radtke S / Kiem HP / Pancera M / McGuire A
History
DepositionJul 3, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71589.png

Downloads & links

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Map

FileDownload / File: emd_71589.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.49 Å/pix.
x 90 pix.
= 404.48 Å		4.49 Å/pix.
x 90 pix.
= 404.48 Å		4.49 Å/pix.
x 90 pix.
= 404.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.49422 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.23
Minimum - Maximum-5.2652726 - 15.694203
Average (Standard dev.)0.007926376 (±0.43327782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 404.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71589_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_71589_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 : Co-expressed EBV glycoprotein gHgL Complex 1:1 with gp42, then co...

EntireName: Co-expressed EBV glycoprotein gHgL Complex 1:1 with gp42, then complex 1:1 with HLA-DR1 BETA CHAIN
Components
  • Complex: Co-expressed EBV glycoprotein gHgL Complex 1:1 with gp42, then complex 1:1 with HLA-DR1 BETA CHAIN
    • Protein or peptide: Surface Glycoprotein gH
    • Protein or peptide: Surface Glycoprotein gL
    • Protein or peptide: Surface Glycoprotein gp42
    • Protein or peptide: HLA class II histocompatibility antigen, DRB1 beta chain

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Supramolecule #1: Co-expressed EBV glycoprotein gHgL Complex 1:1 with gp42, then co...

SupramoleculeName: Co-expressed EBV glycoprotein gHgL Complex 1:1 with gp42, then complex 1:1 with HLA-DR1 BETA CHAIN
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 148.625 KDa

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Macromolecule #1: Surface Glycoprotein gH

MacromoleculeName: Surface Glycoprotein gH / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus) / Strain: B95-8
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQLLCVFCLV LLWEVGAASL SEVKLHLDIE GHASHYTIPW TELMAKVPGL SPEALWREAN VTEDLASMLN RYKLIYKTSG TLGIALAEPV DIPAVSEGSM QVDASKVHPG VISGLNSPAC MLSAPLEKQL FYYIGTMLPN TRPHSYVFYQ LRCHLSYVAL SINGDKFQYT ...String:
MQLLCVFCLV LLWEVGAASL SEVKLHLDIE GHASHYTIPW TELMAKVPGL SPEALWREAN VTEDLASMLN RYKLIYKTSG TLGIALAEPV DIPAVSEGSM QVDASKVHPG VISGLNSPAC MLSAPLEKQL FYYIGTMLPN TRPHSYVFYQ LRCHLSYVAL SINGDKFQYT GAMTSKFLMG TYKRVTEKGD EHVLSLVFGK TKDLPDLRGP FSYPSLTSAQ SGDYSLVIVT TFVHYANFHN YFVPNLKDMF SRAVTMTAAS YARYVLQKLV LLEMKGGCRE PELDTETLTT MFEVSVAFFK VGHAVGETGN GCVDLRWLAK SFFELTVLKD IIGICYGATV KGMQSYGLER LAAMLMATVK MEELGHLTTE KQEYALRLAT VGYPKAGVYS GLIGGATSVL LSAYNRHPLF QPLHTVMRET LFIGSHVVLR ELRLNVTTQG PNLALYQLLS TALCSALEIG EVLRGLALGT ESGLFSPCYL SLRFDLTRDK LLSMAPQEAT LDQAAVSNAV DGFLGRLSLE REDRDAWHLP AYKCVDRLDK VLMIIPLINV TFIISSDREV RGSALYEAST TYLSSSLFLS PVIMNKCSQG AVAGEPRQIP KIQNFTRTQK SCIFCGFALL SYDEKEGLET TTYITSQEVQ NSILSSNYFD FDNLHVHYLL LTTNGTVMEI AGLYEERAHV VLAIILYFIA FALGIFLVHK IVMFFLHHHH HH

UniProtKB: Envelope glycoprotein H

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Macromolecule #2: Surface Glycoprotein gL

MacromoleculeName: Surface Glycoprotein gL / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus) / Strain: B95-8
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MRAVGVFLAI CLVTIFVLPT WGNWAYPCCH VTQLRAQHLL ALENISDIYL VSNQTCDGFS LASLNSPKNG SNQLVISRCA NGLNVVSFFI SILKRSSSAL TGHLRELLTT LETLYGSFSV EDLFGANLNR YAWHRGG

UniProtKB: Envelope glycoprotein L

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Macromolecule #3: Surface Glycoprotein gp42

MacromoleculeName: Surface Glycoprotein gp42 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus) / Strain: B95-8
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVSFKQVRVP LFTAIALVIV LLLAYFLPPR VRGGGRVAAA AITWVPKPNV EVWPVDPPPP VNFNKTAEQE YGDKEVKLPH WTPTLHTFQV PQNYTKANCT YCNTREYTFS YKGCCFYFTK KKHTWNGCFQ ACAELYPCTY FYGPTPDILP VVTRNLNAIE SLWVGVYRVG ...String:
MVSFKQVRVP LFTAIALVIV LLLAYFLPPR VRGGGRVAAA AITWVPKPNV EVWPVDPPPP VNFNKTAEQE YGDKEVKLPH WTPTLHTFQV PQNYTKANCT YCNTREYTFS YKGCCFYFTK KKHTWNGCFQ ACAELYPCTY FYGPTPDILP VVTRNLNAIE SLWVGVYRVG EGNWTSLDGG TFKVYQIFGS HCTYVSKFST VPVSHHECSF LKPCLCVSQR SNSHHHHHH

UniProtKB: Glycoprotein 42

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Macromolecule #4: HLA class II histocompatibility antigen, DRB1 beta chain

MacromoleculeName: HLA class II histocompatibility antigen, DRB1 beta chain
type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAD PGPVSKMRMA TPLLMQAGNS GGGSLVPRGS GGGGSGDTRP RFLWQLKFEC HFFNGTERVR LLERCIYNQE ESVRFDSDVG EYRAVTELGR PDAEYWNSQK DLLEQRRAAV DTYCRHNYGV GESFTVQRRV ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAD PGPVSKMRMA TPLLMQAGNS GGGSLVPRGS GGGGSGDTRP RFLWQLKFEC HFFNGTERVR LLERCIYNQE ESVRFDSDVG EYRAVTELGR PDAEYWNSQK DLLEQRRAAV DTYCRHNYGV GESFTVQRRV EPKVTVYPSK TQPLQHHNLL VCSVSGFYPG SIEVRWFRNG QEEKAGVVST GLIQNGDWTF QTLVMLETVP RSGEVYTCQV EHPSVTSPLT VEWRARSESA QSKSRGGLEV LFQGPVDGGG GGRIARLEEK VKTLKAQNSE LASTANMLRE QVAQLKQKVM NHHHHHHH

UniProtKB: HLA class II histocompatibility antigen, DRB1 beta chain

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 1x TBS
StainingType: NEGATIVE / Material: Uranyl Formate / Details: 2% Uranyl Formate

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Electron microscopy

MicroscopeTFS TALOS L120C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 96000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos L120C / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 3651
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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