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- EMDB-60396: HBcAg-D4 Fab complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60396
TitleHBcAg-D4 Fab complex
Map data
Sample
  • Complex: Asymmetric unit of the complex between HBV capsid and D4 Fab
    • Protein or peptide: Heavy chains of D4 Fab
    • Protein or peptide: Light chains of D4 Fab
    • Protein or peptide: Capsid protein
KeywordsASU / D4 Antibody / HBcAg VLP / VIRUS LIKE PARTICLE / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding
Similarity search - Function
Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / hepatitis B virus genotype C
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhang Z / Ju B / Liu C / Yan H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82025022 China
CitationJournal: J Virol / Year: 2025
Title: The characterization and structural basis of a human broadly binding antibody to HBV core protein.
Authors: Hu Yan / Congcong Liu / Yuxiao Li / Shilong Tang / Huimin Guo / Bing Zhou / Qing Fan / Haiyan Wang / Xiangyang Ge / Xin Wang / Xuejiao Liao / Jin Li / Zheng Zhang / Bin Ju /
Abstract: Hepatitis B virus (HBV) core protein (HBc) plays a crucial role in the virus life cycle, making it an important detection marker for HBV infection and a potential target for treatment. However, ...Hepatitis B virus (HBV) core protein (HBc) plays a crucial role in the virus life cycle, making it an important detection marker for HBV infection and a potential target for treatment. However, several commercially available monoclonal antibodies (mAbs) or polyclonal antibodies (pAbs) targeting HBc have certain limitations in detecting HBV across different genotypes in various biochemical assays, such as enzyme-linked immunosorbent assay, western blot, immunofluorescence assay, flow cytometry, and immune spot assay. In this study, we identified 12 human anti-HBc mAbs and evaluated their potential application in multiple biochemical assays. These mAbs mainly recognized the epitopes near residues 20-22 amino acids (a.a.) and 77-78 a.a. of HBc, demonstrating a broadly cross-genotypic activity. Notably, three Group II mAbs, named cAbA1, cAbD4, and cAbF9, displayed excellent capacities for the detection of HBV infection in all tested biochemical assays. Furthermore, we determined a 3.22 Å of cryo-electron microscopy (cryo-EM) structure of the fragment of antigen binding (Fab) of cAbD4 complexed with HBc dimer, which was the highest resolution of the structural model for Fab-HBc to date. Collectively, our findings provided excellent and reliable antibody candidates for live HBV detection and revealed the recognition mechanism and the detailed interaction information of a potent human anti-HBc mAb binding to the spike tips of HBc dimer.IMPORTANCEThe lack of excellent detection Abs for live hepatitis B virus (HBV) infection and high-resolution structures of the Ab-HBV core protein (HBc) complex largely limited the development of HBV-related research. This study reports a panel of anti-HBc monoclonal antibodies (mAbs) with excellent capacities for detecting HBV infection in multiple biochemical assays and determines a 3.22 Å of cryo-EM structure of HBc with a potent binding mAb. These findings provide excellent and reliable detecting tools for HBV-related research and promote the understanding of the recognition mechanism of anti-HBc mAbs to HBc particles.
History
DepositionJun 4, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60396.png

Downloads & links

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Map

FileDownload / File: emd_60396.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214.8 Å		1.07 Å/pix.
x 200 pix.
= 214.8 Å		1.07 Å/pix.
x 200 pix.
= 214.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0915
Minimum - Maximum-0.0019311165 - 2.1320615
Average (Standard dev.)0.0038963642 (±0.043640103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60396_msk_1.map
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Half map: #2

Fileemd_60396_half_map_1.map
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Half map: #1

Fileemd_60396_half_map_2.map
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Sample components

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Entire : Asymmetric unit of the complex between HBV capsid and D4 Fab

EntireName: Asymmetric unit of the complex between HBV capsid and D4 Fab
Components
  • Complex: Asymmetric unit of the complex between HBV capsid and D4 Fab
    • Protein or peptide: Heavy chains of D4 Fab
    • Protein or peptide: Light chains of D4 Fab
    • Protein or peptide: Capsid protein

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Supramolecule #1: Asymmetric unit of the complex between HBV capsid and D4 Fab

SupramoleculeName: Asymmetric unit of the complex between HBV capsid and D4 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: hepatitis B virus genotype C
Molecular weightTheoretical: 16.097427 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString:
MDIDPYKEFG ASVELLSFLP SDFFPSIRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMNLAT WVGSNLEDPA SRELVVSYV NVNMGLKIRQ LLWFHISCLT FGRETVLEYL VSFGVWIRTP PAYRPPNAPI LST

UniProtKB: Capsid protein

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Macromolecule #2: Heavy chains of D4 Fab

MacromoleculeName: Heavy chains of D4 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.342837 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG VVQPGRSLRL SCAASGFNFN KFGMHWVRQV PGKGLEWLTY IWYDGSNADY VDSVKGRFTI SRDNSINTLY LQMNSLRAD DTAVYFCARG FYDSSSLESW GQGALVIVSS AS

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Macromolecule #3: Light chains of D4 Fab

MacromoleculeName: Light chains of D4 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.504955 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPLS LAVTPGEPAS ISCRSSQTLL HNNGYNYFSW YLQKPGQAPQ LLIYLGSNRA PGVSDRFSGS GSGTSFTLEI SRVEAEDVG VYYCMQGRHT PWTFGQGTKV EIKRT

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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

Concentration3 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 75 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 4137 / Average exposure time: 4.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 817068
Startup modelType of model: EMDB MAP
EMDB ID:

14866

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 193181
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4) / Software - details: non-uniform refine
Final 3D classificationNumber classes: 6 / Avg.num./class: 193181 / Software - Name: RELION (ver. 3.1.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3j2v

chain_id: A, source_name: PDB, initial_model_type: experimental model
chain_id: H, source_name: AlphaFold, initial_model_type: in silico model
chain_id: L, source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient
Output model

PDB-8zrh:
HBcAg-D4 Fab complex

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