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

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Basic information

Entry
Database: PDB / ID: 9ma0
TitleCryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 4A11
Components
  • 4A11 heavy chain
  • 4A11 light chain
  • Envelope glycoprotein GP350
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Envelope glycoprotein GP350 / Membrane antigen (MA) / neutralizing antibody / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsMa, H.Y. / Sun, C.
Funding support China, 2items
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, H.Y. / Sun, C.
History
DepositionMar 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein GP350
B: 4A11 heavy chain
C: 4A11 light chain


Theoretical massNumber of molelcules
Total (without water)103,6003
Polymers103,6003
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Envelope glycoprotein GP350 / Membrane antigen / MA


Mass: 51454.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Gene: BLLF1
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
References: UniProt: P03200
#2: Antibody 4A11 heavy chain


Mass: 26732.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
#3: Antibody 4A11 light chain


Mass: 25413.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 4A11
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))10377
21Homo sapiens (human)9606
Source (recombinant)Organism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.41particle selection
12cryoSPARC4.4.13D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 857731 / Num. of class averages: 476075 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 3.33 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045116
ELECTRON MICROSCOPYf_angle_d0.886983
ELECTRON MICROSCOPYf_dihedral_angle_d5.371694
ELECTRON MICROSCOPYf_chiral_restr0.05787
ELECTRON MICROSCOPYf_plane_restr0.008906

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