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- EMDB-71588: Negative stain EM map of EBV glycoprotein gH/gL in complex with g... -

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Basic information

Entry
Database: EMDB / ID: EMD-71588
TitleNegative stain EM map of EBV glycoprotein gH/gL in complex with glycoprotein gp42 and FAB ATX-42-2 closed conformation
Map data
Sample
  • Complex: coexpress glycoprotein gh/gL complex 1:1 with glycoprotein gp42, then complex 1:1 with FAB ATX-42-2
    • Protein or peptide: surface glycoprotein gH
    • Protein or peptide: surface glycoprotein gL
    • Protein or peptide: surface glycoprotein gp42
    • Protein or peptide: FAB ATX-42-2 heavy chain
    • Protein or peptide: FAB ATX-42-2 light chain
KeywordsViral protein / Complex / Antibody / EBV / IMMUNE SYSTEM
Function / homology
Function and homology information


host cell membrane / carbohydrate binding / host cell Golgi apparatus / receptor ligand activity / 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 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 / Herpesvirus glycoprotein L, rhadinovirus-type ...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 / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Envelope glycoprotein GP350 / Glycoprotein 42 / Envelope glycoprotein L
Similarity search - Component
Biological specieshuman gammaherpesvirus 4 (Epstein-Barr virus) / Mus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 11.6 Å
AuthorsLang K / Kher G / Chan CB / 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_71588.png

Downloads & links

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Map

FileDownload / File: emd_71588.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: 0.796
Minimum - Maximum-2.1084924 - 12.0747
Average (Standard dev.)-0.0037659535 (±0.27930132)
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_71588_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_71588_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 : coexpress glycoprotein gh/gL complex 1:1 with glycoprotein gp42, ...

EntireName: coexpress glycoprotein gh/gL complex 1:1 with glycoprotein gp42, then complex 1:1 with FAB ATX-42-2
Components
  • Complex: coexpress glycoprotein gh/gL complex 1:1 with glycoprotein gp42, then complex 1:1 with FAB ATX-42-2
    • Protein or peptide: surface glycoprotein gH
    • Protein or peptide: surface glycoprotein gL
    • Protein or peptide: surface glycoprotein gp42
    • Protein or peptide: FAB ATX-42-2 heavy chain
    • Protein or peptide: FAB ATX-42-2 light chain

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Supramolecule #1: coexpress glycoprotein gh/gL complex 1:1 with glycoprotein gp42, ...

SupramoleculeName: coexpress glycoprotein gh/gL complex 1:1 with glycoprotein gp42, then complex 1:1 with FAB ATX-42-2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 173 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)
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 GP350

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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: FAB ATX-42-2 heavy chain

MacromoleculeName: FAB ATX-42-2 heavy chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHSSALLCCL VLLTGVRAEV QLVQSGAEVK KPGESLKISC KGSGYSFSNY WIAWVRQMPG KGLEWMGIIY PDDSDTRYSP SFQGQVTISA DKSISTAYLS WSSLKASDTA MYYCAREGDY YYGSGTYYKV WFDPWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL ...String:
MHSSALLCCL VLLTGVRAEV QLVQSGAEVK KPGESLKISC KGSGYSFSNY WIAWVRQMPG KGLEWMGIIY PDDSDTRYSP SFQGQVTISA DKSISTAYLS WSSLKASDTA MYYCAREGDY YYGSGTYYKV WFDPWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPK

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Macromolecule #5: FAB ATX-42-2 light chain

MacromoleculeName: FAB ATX-42-2 light chain / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHSSALLCCL VLLTGVRAEI VLTQSPATLS LSPGERATLS CRASQSVSTY LAWYQQKPGQ APRLLIYDTS NRATGIPARF SGSGSGTDFT LTISSLEPED FAVYYCQQRS NWPLTFGGGT KVEIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN ...String:
MHSSALLCCL VLLTGVRAEI VLTQSPATLS LSPGERATLS CRASQSVSTY LAWYQQKPGQ APRLLIYDTS NRATGIPARF SGSGSGTDFT LTISSLEPED FAVYYCQQRS NWPLTFGGGT KVEIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN ALQSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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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: 92000
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: 11.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 5112
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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