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- EMDB-71593: Negative Stain EM map of EBV glycoprotein gp350 in complex with A... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71593
TitleNegative Stain EM map of EBV glycoprotein gp350 in complex with ATX-350-1 FAB
Map data
Sample
  • Complex: EBV glycoprotein gp350 1:1 ATX-350-1 FAB
    • Protein or peptide: Surface Glycoprotein gp350
    • Protein or peptide: Fab ATX-350-1 light chain
    • Protein or peptide: Fab ATX-350-1 heavy chain
KeywordsViral protein / Complex / Antibody / EBV / IMMUNE SYSTEM
Function / homology
Function and homology information


host cell membrane / receptor ligand activity / symbiont entry into host cell / virion membrane / membrane
Similarity search - Function
Herpesvirus major outer envelope glycoprotein / : / : / : / : / Herpes virus envelope glycoprotein gp350, N-terminal A domain / Herpesvirus envelope glycoprotein gp350, N-terminal B domain / Herpesvirus envelope glycoprotein gp350 N-terminal C domain / Herpesvirus Envelope glycoprotein GP350 C-terminal
Similarity search - Domain/homology
Envelope glycoprotein GP350
Similarity search - Component
Biological specieshuman gammaherpesvirus 4 (Epstein-Barr virus) / Mus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 12.84 Å
AuthorsLang K / 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_71593.png

Downloads & links

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Map

FileDownload / File: emd_71593.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: 1.4
Minimum - Maximum-9.40882 - 19.650541
Average (Standard dev.)-0.006855646 (±0.38585833)
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: mapB

Fileemd_71593_half_map_1.map
AnnotationmapB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: mapA

Fileemd_71593_half_map_2.map
AnnotationmapA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : EBV glycoprotein gp350 1:1 ATX-350-1 FAB

EntireName: EBV glycoprotein gp350 1:1 ATX-350-1 FAB
Components
  • Complex: EBV glycoprotein gp350 1:1 ATX-350-1 FAB
    • Protein or peptide: Surface Glycoprotein gp350
    • Protein or peptide: Fab ATX-350-1 light chain
    • Protein or peptide: Fab ATX-350-1 heavy chain

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Supramolecule #1: EBV glycoprotein gp350 1:1 ATX-350-1 FAB

SupramoleculeName: EBV glycoprotein gp350 1:1 ATX-350-1 FAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 107 KDa

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Macromolecule #1: Surface Glycoprotein gp350

MacromoleculeName: Surface Glycoprotein gp350 / 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: MEAALLVCQY TIQSLIHLTG EDPGFFNVEI PEFPFYPTCN VCTADVNVTI NFDVGGKKHQ LDLDFGQLTP HTKAVYQPRG AFGGSENATN LFLLELLGAG ELALTMRSKK LPINVTTGEE QQVSLESVDV YFQDVFGTMW CHHAEMQNPV YLIPETVPYI KWDNCNSTNI ...String:
MEAALLVCQY TIQSLIHLTG EDPGFFNVEI PEFPFYPTCN VCTADVNVTI NFDVGGKKHQ LDLDFGQLTP HTKAVYQPRG AFGGSENATN LFLLELLGAG ELALTMRSKK LPINVTTGEE QQVSLESVDV YFQDVFGTMW CHHAEMQNPV YLIPETVPYI KWDNCNSTNI TAVVRAQGLD VTLPLSLPTS AQDSNFSVKT QMLGNEIDIE CIMEDGEISQ VLPGDNKFNI TCSGYESHVP SGGILTSTSP VATPIPGTGY AYSLRLTPRP VSRFLGNNSI LYVFYSGNGP KASGGDYCIQ SNIVFSDEIP ASQDMPTNTT DITYVGDNAT YSVPMVTSED ANSPNVTVTA FWAWPNNTET DFKCKWTLTS GTPSGCENIS GAFASNRTFD ITVSGLGTAP KTLIITRTAT NATTTTHKVI FSKAPESTTT SPTLNTTGFA DPNTTTGLPS STHVPTNLTA PASTGPTVST

UniProtKB: Envelope glycoprotein GP350

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Macromolecule #2: Fab ATX-350-1 light chain

MacromoleculeName: Fab ATX-350-1 light chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHSSALLCCL VLLTGVRADI QMTQSPSSIS ASVGDRLTIT CRASQGISRW LAWYQQKPGK APKLLIYASS NLQSGVPSRF SGGGFGTEFT LTISSLQPED FATYYCQQAN SFPYTFGQGT KLEIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN ...String:
MHSSALLCCL VLLTGVRADI QMTQSPSSIS ASVGDRLTIT CRASQGISRW LAWYQQKPGK APKLLIYASS NLQSGVPSRF SGGGFGTEFT LTISSLQPED FATYYCQQAN SFPYTFGQGT KLEIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN ALQSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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Macromolecule #3: Fab ATX-350-1 heavy chain

MacromoleculeName: Fab ATX-350-1 heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHSSALLCCL VLLTGVRAEV QLVESGGGLV QPGRSLRLSC AASGFTFNTY AMYWVRQAPG KGLEWVSGIS WNSGSIGYAD SVKGRFTISR DNAKNSLYLQ MNSLRIEDTA LYYCAKGRTA NTSFDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF ...String:
MHSSALLCCL VLLTGVRAEV QLVESGGGLV QPGRSLRLSC AASGFTFNTY AMYWVRQAPG KGLEWVSGIS WNSGSIGYAD SVKGRFTISR DNAKNSLYLQ MNSLRIEDTA LYYCAKGRTA NTSFDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKP

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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

Concentration0.02 mg/mL
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: 12.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 1847
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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