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- PDB-8yy6: Structure of a murine monoclonal antibody Fab5 targeting Epstein-... -

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Basic information

Entry
Database: PDB / ID: 8yy6
TitleStructure of a murine monoclonal antibody Fab5 targeting Epstein-Barr virus gB
Components
  • BALF4
  • Fab5 H chain
  • Fab5 L chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / EBV / Antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endosome / host cell Golgi apparatus / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
: / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
human gammaherpesvirus 4 (Epstein-Barr virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFang, X.Y. / Sun, C. / Zeng, M.S. / Liu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: Adv Mater / Year: 2025
Title: Chimeric Glycoprotein Nanoparticles Elicit Robust Neutralizing Antibodies Against Epstein-Barr Virus.
Authors: Cong Sun / Chu Xie / Xin-Yan Fang / Dong-Chun Hong / Haoyu Zhang / Pei-Huang Wu / Yi-Na Liu / Guo-Long Bu / De-Hai Cao / Min-Yi Si-Tu / Yong-Jian Peng / Jing Wang / Guo-Kai Feng / Qian Zhong ...Authors: Cong Sun / Chu Xie / Xin-Yan Fang / Dong-Chun Hong / Haoyu Zhang / Pei-Huang Wu / Yi-Na Liu / Guo-Long Bu / De-Hai Cao / Min-Yi Si-Tu / Yong-Jian Peng / Jing Wang / Guo-Kai Feng / Qian Zhong / Zheng Liu / Mu-Sheng Zeng /
Abstract: Epstein‒Barr virus (EBV) is a ubiquitous gammaherpesvirus linked to a broad spectrum of malignancies and autoimmune diseases with no approved therapeutic drugs or vaccines. EBV infection relies on ...Epstein‒Barr virus (EBV) is a ubiquitous gammaherpesvirus linked to a broad spectrum of malignancies and autoimmune diseases with no approved therapeutic drugs or vaccines. EBV infection relies on the viral glycoproteins gB and gHgL, which, together, function as the fusion apparatus, mediating viral recognition and membrane fusion in both epithelial and B cells. Despite discovering potent neutralizing antibodies targeting gB and gHgL, the heterogeneous antigen structures and distribution of multiple glycoproteins in the virion hinder rational vaccine design targeting this apparatus complex. In this study, Chimeric nanoparticles (Chimeric-NPs) are designed that co-display EBV fusion apparatus and induce significantly more neutralizing antibodies in mice and nonhuman primates than the cocktail counterparts. It is further demonstrated that the Chimeric-NPs elicited neutralizing antibodies predominantly targeting gB, closely mimicking the antibody induction pattern by the whole EBV virion. Additionally, single-BCR sequencing is used to analyze the B cell response to Chimeric-NP, and a novel gB neutralizing antibody Fab5 targeting a new vulnerable site EBV gB is identified. These findings provide novel candidates and vaccine design strategies for EBV and reveal the underlying mechanisms of antibody induction and immune response regulation by chimera vaccines, with potential implications for all multi-antigen-harbored pathogens.
History
DepositionApr 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Fab5 H chain
F: Fab5 L chain
A: BALF4
E: Fab5 H chain
H: Fab5 L chain
B: BALF4
G: Fab5 H chain
I: Fab5 L chain
C: BALF4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,69412
Polymers368,0309
Non-polymers6643
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: Antibody Fab5 H chain


Mass: 24199.873 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab5 L chain


Mass: 23261.846 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein BALF4 / gB / Glycoprotein gp110


Mass: 75215.109 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human gammaherpesvirus 4 (Epstein-Barr virus)
Gene: BALF4 / Production host: Homo sapiens (human) / References: UniProt: R4R670
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Complex of glycoprotein B with fab5 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Human herpesvirus 4 (Epstein-Barr virus)10376
31Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 184393 / Symmetry type: POINT

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