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- EMDB-63748: Cryo-EM structure of EBV gp350 D123 in complex with neutralizing ... -

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Basic information

Entry
Database: EMDB / ID: EMD-63748
TitleCryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9
Map data
Sample
  • Complex: Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9
    • Protein or peptide: Envelope glycoprotein GP350
    • Protein or peptide: 1H5 heavy chain no-CH2CH3
    • Protein or peptide: 1H5 light chain
    • Protein or peptide: 1A12 heavy chain no-CH2CH3
    • Protein or peptide: 1A12 light chain
    • Protein or peptide: 2E9 heavy chain no-CH2CH3
    • Protein or peptide: 2E9 light chain
KeywordsEnvelope glycoprotein GP350 / Membrane antigen (MA) / neutralizing antibody / 1A22 / 1E5 / 2E9 / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell membrane / receptor ligand activity / symbiont entry into host cell / virion 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) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsMa HY / Sun C
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U24A20743 China
National Natural Science Foundation of China (NSFC)32441094 China
CitationJournal: To Be Published
Title: Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9
Authors: Ma HY / Sun C
History
DepositionMar 14, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63748.png

Downloads & links

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Map

FileDownload / File: emd_63748.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.001657465 - 2.335621
Average (Standard dev.)0.0012084594 (±0.024533339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63748_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63748_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63748_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 : Cryo-EM structure of EBV gp350 D123 in complex with neutralizing ...

EntireName: Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9
Components
  • Complex: Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9
    • Protein or peptide: Envelope glycoprotein GP350
    • Protein or peptide: 1H5 heavy chain no-CH2CH3
    • Protein or peptide: 1H5 light chain
    • Protein or peptide: 1A12 heavy chain no-CH2CH3
    • Protein or peptide: 1A12 light chain
    • Protein or peptide: 2E9 heavy chain no-CH2CH3
    • Protein or peptide: 2E9 light chain

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Supramolecule #1: Cryo-EM structure of EBV gp350 D123 in complex with neutralizing ...

SupramoleculeName: Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus)

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Macromolecule #1: Envelope glycoprotein GP350

MacromoleculeName: Envelope glycoprotein GP350 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus)
Molecular weightTheoretical: 51.454 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: MEAALLVCQY TIQSLIHLTG EDPGFFNVEI PEFPFYPTCN VCTADVNVTI NFDVGGKKHQ LDLDFGQLTP HTKAVYQPRG AFGGSENAT NLFLLELLGA GELALTMRSK KLPINVTTGE EQQVSLESVD VYFQDVFGTM WCHHAEMQNP VYLIPETVPY I KWDNCNST ...String:
MEAALLVCQY TIQSLIHLTG EDPGFFNVEI PEFPFYPTCN VCTADVNVTI NFDVGGKKHQ LDLDFGQLTP HTKAVYQPRG AFGGSENAT NLFLLELLGA GELALTMRSK KLPINVTTGE EQQVSLESVD VYFQDVFGTM WCHHAEMQNP VYLIPETVPY I KWDNCNST NITAVVRAQG LDVTLPLSLP TSAQDSNFSV KTQMLGNEID IECIMEDGEI SQVLPGDNKF NITCSGYESH VP SGGILTS TSPVATPIPG TGYAYSLRLT PRPVSRFLGN NSILYVFYSG NGPKASGGDY CIQSNIVFSD EIPASQDMPT NTT DITYVG DNATYSVPMV TSEDANSPNV TVTAFWAWPN NTETDFKCKW TLTSGTPSGC ENISGAFASN RTFDITVSGL GTAP KTLII TRTATNATTT THKVIFSKAP ESTTTSPTLN TTGFADPNTT TGLPSSTHVP TNLTAPASTG PTVSTGSHHH HHH

UniProtKB: Envelope glycoprotein GP350

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Macromolecule #2: 1H5 heavy chain no-CH2CH3

MacromoleculeName: 1H5 heavy chain no-CH2CH3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.27152 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: MGWSCIILFL VATATGVHSQ VQLVQSGAEV RKPGSSVKVS CEFSGGPFKN SAFSWVRQAP GQGPEWMGGI IPPFVRGKYA QGFQGRVTI TADEHLSTTY MELTGLRSDD TAVYYCARGP SSGNYNYYYG MDVWGQGTPV SVSSASTKGP SVFPLAPSSK S TSGGTAAL ...String:
MGWSCIILFL VATATGVHSQ VQLVQSGAEV RKPGSSVKVS CEFSGGPFKN SAFSWVRQAP GQGPEWMGGI IPPFVRGKYA QGFQGRVTI TADEHLSTTY MELTGLRSDD TAVYYCARGP SSGNYNYYYG MDVWGQGTPV SVSSASTKGP SVFPLAPSSK S TSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KR VEPKSCD K

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Macromolecule #3: 1H5 light chain

MacromoleculeName: 1H5 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.930629 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: MGWSCIILFL VATATGSWAQ SVLTQPPSAS GTPGQRVTIS CSGSSSNIGS NYVYWYQQLP GTAPKLLIYR NNQRPSGVPD RFSGSKSGT SASLAISGLR SEDEADYYCA AWDDSLSGWV FGGGTQLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT ...String:
MGWSCIILFL VATATGSWAQ SVLTQPPSAS GTPGQRVTIS CSGSSSNIGS NYVYWYQQLP GTAPKLLIYR NNQRPSGVPD RFSGSKSGT SASLAISGLR SEDEADYYCA AWDDSLSGWV FGGGTQLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT VAWKADSSPV KAGVETTTPS KQSNNKYAAS SYLSLTPEQW KSHRSYSCQV THEGSTVEKT VAPTECS

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Macromolecule #4: 1A12 heavy chain no-CH2CH3

MacromoleculeName: 1A12 heavy chain no-CH2CH3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.62107 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: MGWSCIILFL VATATGVHSQ VQLVQSGAEV KKPGASMKVS CKASGYTFAG YYIHWVRQAP GQGLEWMGSI NPNSGKATYA QRFHGRVTL TREMSINTAY MELTRLTSDD TAIYYCARDA TYSTSFSPRW FDPWGQGTLV TVSSASTKGP SVFPLAPSSK S TSGGTAAL ...String:
MGWSCIILFL VATATGVHSQ VQLVQSGAEV KKPGASMKVS CKASGYTFAG YYIHWVRQAP GQGLEWMGSI NPNSGKATYA QRFHGRVTL TREMSINTAY MELTRLTSDD TAIYYCARDA TYSTSFSPRW FDPWGQGTLV TVSSASTKGP SVFPLAPSSK S TSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KR VEPKSCD K

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Macromolecule #5: 1A12 light chain

MacromoleculeName: 1A12 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.901787 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: MGWSCIILFL VATATGSWAE IVLTQSPGTL SLSPGERATL SCRASQSISS NSLAWYQQRP GQAPRLLIYG ASSRATGIPD RFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGSSPRTFG PGTKVDIKGQ PKAAPSVTLF PPSSEELQAN KATLVCLISD F YPGAVTVA ...String:
MGWSCIILFL VATATGSWAE IVLTQSPGTL SLSPGERATL SCRASQSISS NSLAWYQQRP GQAPRLLIYG ASSRATGIPD RFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGSSPRTFG PGTKVDIKGQ PKAAPSVTLF PPSSEELQAN KATLVCLISD F YPGAVTVA WKADSSPVKA GVETTTPSKQ SNNKYAASSY LSLTPEQWKS HRSYSCQVTH EGSTVEKTVA PTECS

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Macromolecule #6: 2E9 heavy chain no-CH2CH3

MacromoleculeName: 2E9 heavy chain no-CH2CH3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.906123 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: MGWSCIILFL VATATGVHSQ VQLQESGPGL VKPSETLSLI CTVSGYSISS GYNWGWIRQP PGKGLEWIGS INHSGSTYYN PSLKSRVTT SVDTSTNQFS LKLSSVTAAD TAVYYCARDS IMIGYRGLDY WGQGTLVSVS SASTKGPSVF PLAPSSKSTS G GTAALGCL ...String:
MGWSCIILFL VATATGVHSQ VQLQESGPGL VKPSETLSLI CTVSGYSISS GYNWGWIRQP PGKGLEWIGS INHSGSTYYN PSLKSRVTT SVDTSTNQFS LKLSSVTAAD TAVYYCARDS IMIGYRGLDY WGQGTLVSVS SASTKGPSVF PLAPSSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EP KSCDK

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Macromolecule #7: 2E9 light chain

MacromoleculeName: 2E9 light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.774502 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: MGWSCIILFL VATATGSWAQ SVVTQPPSVS AAPGQKVTIS CSGSSSNIGN NYVSWYQQLP GTAPKLLIYD NNKRPSGIPD RFSGSKSGT SATLGITGLQ TGDEADYYCG TWDSSLSAYV FGTGTQLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT ...String:
MGWSCIILFL VATATGSWAQ SVVTQPPSVS AAPGQKVTIS CSGSSSNIGN NYVSWYQQLP GTAPKLLIYD NNKRPSGIPD RFSGSKSGT SATLGITGLQ TGDEADYYCG TWDSSLSAYV FGTGTQLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT VAWKADSSPV KAGVETTTPS KQSNNKYAAS SYLSLTPEQW KSHRSYSCQV THEGSTVEKT VAPTECS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 266743 / Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 673171
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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