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- EMDB-63745: Cryo-EM structure of EBV gp350 D123 in complex with neutralizing ... -

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Basic information

Entry
Database: EMDB / ID: EMD-63745
TitleCryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 4A11
Map data
Sample
  • Complex: Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 4A11
    • Protein or peptide: Envelope glycoprotein GP350
    • Protein or peptide: 4A11 heavy chain
    • Protein or peptide: 4A11 light chain
KeywordsEnvelope glycoprotein GP350 / Membrane antigen (MA) / neutralizing antibody / 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 herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 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 4A11
Authors: Ma HY / Sun C
History
DepositionMar 13, 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_63745.png

Downloads & links

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Map

FileDownload / File: emd_63745.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 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: 0.2
Minimum - Maximum-0.0016898045 - 2.4975853
Average (Standard dev.)0.0015715543 (±0.029260185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63745_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63745_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_63745_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 4A11
Components
  • Complex: Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 4A11
    • Protein or peptide: Envelope glycoprotein GP350
    • Protein or peptide: 4A11 heavy chain
    • Protein or peptide: 4A11 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 4A11
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))

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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 herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
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: 4A11 heavy chain

MacromoleculeName: 4A11 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.732086 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: MGWSCIILFL VATATGVHSQ VQLVQSGAEV KKPGASVKVS CKASGYTFTG YYIHWVRQAP GQGLEWMGWM NPNSGATNYA QKFQGRVTM TRDTSINTAY MELSSLRSDD TAVYFCAKDP RYSSSWRHNW FDPWGQGTLV SVSSASTKGP SVFPLAPSSK S TSGGTAAL ...String:
MGWSCIILFL VATATGVHSQ VQLVQSGAEV KKPGASVKVS CKASGYTFTG YYIHWVRQAP GQGLEWMGWM NPNSGATNYA QKFQGRVTM TRDTSINTAY MELSSLRSDD TAVYFCAKDP RYSSSWRHNW FDPWGQGTLV SVSSASTKGP SVFPLAPSSK S TSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KR VEPKSCD K

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Macromolecule #3: 4A11 light chain

MacromoleculeName: 4A11 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.413547 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: MGWSCIILFL VATATGSWAD IVLTQSPLSL TVTPGEPASI SCRSSQSLLH SSGHNFLSWY LQKPGQSPQL LIYLGSNRAS GVPDRFSGS GTGADFTLKI SRVEAEDVGV YYCLQTLRAP FTFGQGTRLE IKGQPKAAPS VTLFPPSSEE LQANKATLVC L ISDFYPGA ...String:
MGWSCIILFL VATATGSWAD IVLTQSPLSL TVTPGEPASI SCRSSQSLLH SSGHNFLSWY LQKPGQSPQL LIYLGSNRAS GVPDRFSGS GTGADFTLKI SRVEAEDVGV YYCLQTLRAP FTFGQGTRLE IKGQPKAAPS VTLFPPSSEE LQANKATLVC L ISDFYPGA VTVAWKADSS PVKAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

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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: 1.2 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: 476075 / Resolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 857731
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9ma0:
Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 4A11

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