+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-60396 | |||||||||
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Title | HBcAg-D4 Fab complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ASU / 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 | |||||||||
Biological species | Homo sapiens (human) / hepatitis B virus genotype C | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Zhang Z / Ju B / Liu C / Yan H | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: HBcAg-D4 Fab complex Authors: Zhang Z / Ju B / Liu C / Yan H | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_60396.map.gz | 27.3 MB | EMDB map data format | |
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Header (meta data) | emd-60396-v30.xml emd-60396.xml | 19.9 KB 19.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_60396_fsc.xml | 6.5 KB | Display | FSC data file |
Images | emd_60396.png | 50.9 KB | ||
Masks | emd_60396_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-60396.cif.gz | 6.2 KB | ||
Others | emd_60396_half_map_1.map.gz emd_60396_half_map_2.map.gz | 28.4 MB 28.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60396 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60396 | HTTPS FTP |
-Validation report
Summary document | emd_60396_validation.pdf.gz | 843.5 KB | Display | EMDB validaton report |
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Full document | emd_60396_full_validation.pdf.gz | 843.1 KB | Display | |
Data in XML | emd_60396_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_60396_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60396 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60396 | HTTPS FTP |
-Related structure data
Related structure data | 8zrhMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_60396.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.074 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_60396_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_60396_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60396_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Asymmetric unit of the complex between HBV capsid and D4 Fab
Entire | Name: Asymmetric unit of the complex between HBV capsid and D4 Fab |
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Components |
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-Supramolecule #1: Asymmetric unit of the complex between HBV capsid and D4 Fab
Supramolecule | Name: Asymmetric unit of the complex between HBV capsid and D4 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: hepatitis B virus genotype C |
Molecular weight | Theoretical: 16.097427 KDa |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
Sequence | String: MDIDPYKEFG ASVELLSFLP SDFFPSIRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMNLAT WVGSNLEDPA SRELVVSYV NVNMGLKIRQ LLWFHISCLT FGRETVLEYL VSFGVWIRTP PAYRPPNAPI LST UniProtKB: Capsid protein |
-Macromolecule #2: Heavy chains of D4 Fab
Macromolecule | Name: Heavy chains of D4 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.342837 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVESGGG VVQPGRSLRL SCAASGFNFN KFGMHWVRQV PGKGLEWLTY IWYDGSNADY VDSVKGRFTI SRDNSINTLY LQMNSLRAD DTAVYFCARG FYDSSSLESW GQGALVIVSS AS |
-Macromolecule #3: Light chains of D4 Fab
Macromolecule | Name: Light chains of D4 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.504955 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIVMTQSPLS LAVTPGEPAS ISCRSSQTLL HNNGYNYFSW YLQKPGQAPQ LLIYLGSNRA PGVSDRFSGS GSGTSFTLEI SRVEAEDVG VYYCMQGRHT PWTFGQGTKV EIKRT |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: 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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient | ||||||||
Output model | PDB-8zrh: |