[English] 日本語
Yorodumi- EMDB-14348: 64K CDS Apoferritin map reconstructed from 32.5K sub-tomograms wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14348 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 64K CDS Apoferritin map reconstructed from 32.5K sub-tomograms with emClarity | |||||||||
Map data | sharpened emClarity map | |||||||||
Sample |
| |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Clare DK | |||||||||
Funding support | United Kingdom, 1 items
| |||||||||
Citation | Journal: To Be Published Title: 2.7 A STRUCTURE OF HUMAN APOFERRITIN OBTAINED FROM TITAN KRIOS 2 AT eBIC, DLS UNDER COMMISSIONING SESSION CM26464-2 USING SUB-TOMOGRAM AVERAGING Authors: Clare DK | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_14348.map.gz | 3.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-14348-v30.xml emd-14348.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14348_fsc.xml | 6.8 KB | Display | FSC data file |
Images | emd_14348.png | 296.8 KB | ||
Others | emd_14348_additional_1.map.gz | 2.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14348 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14348 | HTTPS FTP |
-Validation report
Summary document | emd_14348_validation.pdf.gz | 413.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_14348_full_validation.pdf.gz | 412.7 KB | Display | |
Data in XML | emd_14348_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | emd_14348_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14348 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14348 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_14348.map.gz / Format: CCP4 / Size: 21.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpened emClarity map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.356 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Relion sharpened emClarity/CisTEM map
File | emd_14348_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Relion sharpened emClarity/CisTEM map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : human Apoferritin
Entire | Name: human Apoferritin |
---|---|
Components |
|
-Supramolecule #1: human Apoferritin
Supramolecule | Name: human Apoferritin / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 / Details: Heavy chain |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 500 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
---|---|
Buffer | pH: 7.5 / Details: 50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM TCEP |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time of 2.5 seconds. |
Details | The apoferritin sample was applied to in-house graphene-coated Quantifoil r2/2 EM grid |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Details | Dose symmetric tilt series |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Average exposure time: 0.6 sec. / Average electron dose: 2.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 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 / Nominal magnification: 64000 |
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 | PDB ID: |
---|---|
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |