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Yorodumi- EMDB-6745: Cryo-EM structure of complex of HBsAg and Fab fragment of therape... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6745 | |||||||||
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Title | Cryo-EM structure of complex of HBsAg and Fab fragment of therapeutic mAb-E6F6. | |||||||||
Map data | Cryo-EM structure of HBsAg-E6F6-Fab complex | |||||||||
Sample |
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Biological species | Drosophila (fruit flies) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Mo X / Yuan AY | |||||||||
Citation | Journal: To be published Title: Structural insight into mechanism of antibody-mediated immunotherapy for persistent hepatitis B virus infection Authors: Mo X / Yuan YA | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6745.map.gz | 17.5 MB | EMDB map data format | |
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Header (meta data) | emd-6745-v30.xml emd-6745.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6745_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_6745.png | 213.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6745 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6745 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6745.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of HBsAg-E6F6-Fab complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.81 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of HBsAg with Fab fragment of therapeutic mAb-E6F6
Entire | Name: Complex of HBsAg with Fab fragment of therapeutic mAb-E6F6 |
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Components |
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-Supramolecule #1: Complex of HBsAg with Fab fragment of therapeutic mAb-E6F6
Supramolecule | Name: Complex of HBsAg with Fab fragment of therapeutic mAb-E6F6 type: complex / ID: 1 / Parent: 0 Details: Surface protein of Hepatitis B virus and fab fragment generated by proteolytic cleavage of therapeutic mAb-E6F6. |
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Source (natural) | Organism: Drosophila (fruit flies) |
Recombinant expression | Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) Recombinant strain: DH5a / Recombinant plasmid: pET-Duet |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Molecular weight | Experimental: 3.24 MDa |
-Supramolecule #2: HBsAg
Supramolecule | Name: HBsAg / type: complex / ID: 2 / Parent: 1 / Details: Surface protein of Hepatitis B virus. |
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-Supramolecule #3: E6F6-Fab
Supramolecule | Name: E6F6-Fab / type: complex / ID: 3 / Parent: 1 Details: Fab fragment generated by proteolytic cleavage of therapeutic mAb-E6F6. |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||
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Buffer | pH: 6.5 Component:
Details: 20mM Tris (pH 6.5), 500mM NaCl | |||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 seconds before pluning. | |||||||||
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 47000 / Illumination mode: OTHER / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 70.0 K / Max: 70.0 K |
Details | Preliminary grid screening was performed manually. |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Number grids imaged: 12 / Number real images: 500 / Average exposure time: 1.0 sec. / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 300 |
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