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- EMDB-60396: HBcAg-D4 Fab complex -

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ID or keywords:

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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: To Be Published
Title: HBcAg-D4 Fab complex
Authors: Zhang Z / Ju B / Liu C / Yan H
History
DepositionJun 4, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density
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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_60396_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_60396_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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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:
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

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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