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- EMDB-39670: Structure of a murine monoclonal antibody Fab5 targeting Epstein-... -

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Basic information

Entry
Database: EMDB / ID: EMD-39670
TitleStructure of a murine monoclonal antibody Fab5 targeting Epstein-Barr virus gB
Map data
Sample
  • Complex: Complex of glycoprotein B with fab5
    • Protein or peptide: Fab5 H chain
    • Protein or peptide: Fab5 L chain
    • Protein or peptide: BALF4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsEBV / Antibody / VIRAL PROTEIN/IMMUNE SYSTEM / 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 speciesHuman herpesvirus 4 (Epstein-Barr virus) / Homo sapiens (human) / human gammaherpesvirus 4 (Epstein-Barr virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFang XY / Sun C / Zeng MS / Liu Z
Funding support China, 1 items
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, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39670.png

Downloads & links

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Map

FileDownload / File: emd_39670.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.29946652 - 0.6871864
Average (Standard dev.)0.00032658913 (±0.0142146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39670_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_39670_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 : Complex of glycoprotein B with fab5

EntireName: Complex of glycoprotein B with fab5
Components
  • Complex: Complex of glycoprotein B with fab5
    • Protein or peptide: Fab5 H chain
    • Protein or peptide: Fab5 L chain
    • Protein or peptide: BALF4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of glycoprotein B with fab5

SupramoleculeName: Complex of glycoprotein B with fab5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human herpesvirus 4 (Epstein-Barr virus)

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Macromolecule #1: Fab5 H chain

MacromoleculeName: Fab5 H chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.199873 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQPGAE LVRPGASVKL SCKASGFTFT SYWINWVKQR PGQGLEWIGN IFPSDSYTNY NQKFKDKATL TVDKSSSTAY MLLSSPTSE DSAVYYCTRG GYRYDSDYWG QGTTLTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLQQPGAE LVRPGASVKL SCKASGFTFT SYWINWVKQR PGQGLEWIGN IFPSDSYTNY NQKFKDKATL TVDKSSSTAY MLLSSPTSE DSAVYYCTRG GYRYDSDYWG QGTTLTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVGS HHHHHH

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Macromolecule #2: Fab5 L chain

MacromoleculeName: Fab5 L chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.261846 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIVLTQSPAI MSASPGEKVT MTCSASSSVT YMYWYQQKPG SSPRLLIYDT SNLASGVPVR FSGSGSGTSY SLTISRMEAE DAATYYCQQ WSSYPYTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
QIVLTQSPAI MSASPGEKVT MTCSASSSVT YMYWYQQKPG SSPRLLIYDT SNLASGVPVR FSGSGSGTSY SLTISRMEAE DAATYYCQQ WSSYPYTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #3: BALF4

MacromoleculeName: BALF4 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus)
Molecular weightTheoretical: 75.215109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QTPEQPAPPA TTVQPTATRQ QTSFPFRVCE LSSHGDLFRF SSDIQCPSFG TRENHTEGLL MVFKDNIIPY SFKVRSYTKI VTNILIYNG HRADSVTNRH EEKFSVESYE TDQMDTIYQC YNAVKMTKDG LTRVYVDRDG VNITVNLKPT GGLANGVRRY A SQTELYDA ...String:
QTPEQPAPPA TTVQPTATRQ QTSFPFRVCE LSSHGDLFRF SSDIQCPSFG TRENHTEGLL MVFKDNIIPY SFKVRSYTKI VTNILIYNG HRADSVTNRH EEKFSVESYE TDQMDTIYQC YNAVKMTKDG LTRVYVDRDG VNITVNLKPT GGLANGVRRY A SQTELYDA PGRVEATYRT RTTVNCLITD MMAKSNSPFD FFVTTTGQTV EMSPFYDGKN TETFHERADS FHVRTNYKIV DY DNRGTNP QGERRAFLDK GTYTLSWKLE NRTAYCPLQH WQTFDSTIAT ETGKSIHFVT DEGTSSFVTN TTVGIELPDA FKC IEEQVN KTMHEKYEAV QDRYTKGQEA ITYFITSGGL LLAWLPLTPR SLATVKNLTE LTTPTSSPPS SPSPPAPPAA RGST SAAVL RRRRRNAGNA TTPVPPAAPG KSLGTLNNPA TVQIQFAYDS LRRQINRMLG DLARAWCLEQ KRQNMVLREL TKINP TTVM SSIYGKAVAA KRLGDVISVS QCVPVNQATV TLRKSMRVPG SETMCYSRPL VSFSFINDTK TYEGQLGTDN EIFLTK KMT EVCQATSQYY FQSGNEIHVY NDYHHFKTIE LDGIATLQTF ISLNTSLIEN IDFASLELYS RDEQRASNVF DLEGIFR EY NFQAQNIAGL RKDLDNAVSH HHHHH

UniProtKB: BALF4

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 184393
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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