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- PDB-8khr: Cryo-EM structure of EBV gH/gL-gp42 in complex with fab 2C1 -

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Basic information

Entry
Database: PDB / ID: 8khr
TitleCryo-EM structure of EBV gH/gL-gp42 in complex with fab 2C1
Components
  • 2C1 heavy chain
  • 2C1 light chain
  • Envelope glycoprotein H
  • Envelope glycoprotein L
  • Soluble gp42
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Human gammaherpesvirus 4 / Neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell membrane / host cell endosome / carbohydrate binding / host cell Golgi apparatus / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Gammaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain ...Gammaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
BKRF2 / BXLF2 / Glycoprotein 42
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsFang, X.Y. / Zhao, G.X. / Zeng, M.S. / Liu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Cell Rep Med / Year: 2024
Title: Potent human monoclonal antibodies targeting Epstein-Barr virus gp42 reveal vulnerable sites for virus infection.
Authors: Ge-Xin Zhao / Xin-Yan Fang / Guo-Long Bu / Shuai-Jia-Bin Chen / Cong Sun / Ting Li / Chu Xie / Yu Wang / Shu-Xin Li / Ning Meng / Guo-Kai Feng / Qian Zhong / Xiang-Wei Kong / Zheng Liu / Mu-Sheng Zeng /
Abstract: Epstein-Barr virus (EBV) is linked to various malignancies and autoimmune diseases, posing a significant global health challenge due to the lack of specific treatments or vaccines. Despite its ...Epstein-Barr virus (EBV) is linked to various malignancies and autoimmune diseases, posing a significant global health challenge due to the lack of specific treatments or vaccines. Despite its crucial role in EBV infection in B cells, the mechanisms of the glycoprotein gp42 remain elusive. In this study, we construct an antibody phage library from 100 EBV-positive individuals, leading to the identification of two human monoclonal antibodies, 2B7 and 2C1. These antibodies effectively neutralize EBV infection in vitro and in vivo while preserving gp42's interaction with the human leukocyte antigen class II (HLA-II) receptor. Structural analysis unveils their distinct binding epitopes on gp42, different from the HLA-II binding site. Furthermore, both 2B7 and 2C1 demonstrate potent neutralization of EBV infection in HLA-II-positive epithelial cells, expanding our understanding of gp42's role. Overall, this study introduces two human anti-gp42 antibodies with potential implications for developing EBV vaccines targeting gp42 epitopes, addressing a critical gap in EBV research.
History
DepositionAug 22, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Soluble gp42
H: 2C1 heavy chain
L: 2C1 light chain
A: Envelope glycoprotein H
B: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)130,5855
Polymers130,5855
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 Soluble gp42


Mass: 22398.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Gene: BZLF2 / Production host: Homo sapiens (human) / References: UniProt: P0C6Z5
#2: Antibody 2C1 heavy chain


Mass: 11978.212 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 2C1 light chain


Mass: 11849.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Protein Envelope glycoprotein H / gH


Mass: 72600.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Gene: BXLF2, gH / Production host: Homo sapiens (human) / References: UniProt: A0A0C7TVV8
#5: Protein Envelope glycoprotein L / gL


Mass: 11759.323 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Gene: BKRF2, gL / Production host: Homo sapiens (human) / References: UniProt: A0A0C7TRA4

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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: Pentamer complex of gH/gL-gp42 with fab 2C1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227428 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028513
ELECTRON MICROSCOPYf_angle_d0.51511619
ELECTRON MICROSCOPYf_dihedral_angle_d3.5851218
ELECTRON MICROSCOPYf_chiral_restr0.0391362
ELECTRON MICROSCOPYf_plane_restr0.0031484

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