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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21708 | |||||||||
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Title | Cu(I)-bound Copper Storage Protein BsCsp3 | |||||||||
![]() | BsCSP3 Density Map | |||||||||
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![]() | small protein (47 kDa) / Z-contrast enhancement in cryo-EM / copper storage protein / metal binding protein | |||||||||
Function / homology | Protein of unknown function DUF326 / Domain of Unknown Function (DUF326) / Uncharacterized cysteine-rich protein YhjQ-like / Uncharacterized cysteine-rich protein YhjQ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Chen JZ / Oken A | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Cu(I)-bound Copper Storage Protein BsCsp3 Authors: Chen JZ / Dennison C | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.7 KB 19.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 4.5 KB | Display | ![]() |
Images | ![]() | 194.5 KB | ||
Masks | ![]() | 3.4 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 1.7 MB 1.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 619 KB | Display | ![]() |
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Full document | ![]() | 618.5 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wktMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | BsCSP3 Density Map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.296 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: BsCSP3 half map - even
File | emd_21708_half_map_1.map | ||||||||||||
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Annotation | BsCSP3 half map - even | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: BsCSP3 half map - odd
File | emd_21708_half_map_2.map | ||||||||||||
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Annotation | BsCSP3 half map - odd | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : BsCsp3, Cu(I) ions
Entire | Name: BsCsp3, Cu(I) ions |
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Components |
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-Supramolecule #1: BsCsp3, Cu(I) ions
Supramolecule | Name: BsCsp3, Cu(I) ions / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 47 KDa |
-Macromolecule #1: Csp3
Macromolecule | Name: Csp3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.853758 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEQYSEACIE ACIDCMKACN HCFTKCLEES VQHHLSGCIR LDRECADICA LAVKAMQTDS PFMKEICALC ADICEACGTE CGKHDHDHC QACAKACFTC AEQCRSMAA UniProtKB: Uncharacterized cysteine-rich protein YhjQ |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.11 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 15 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa / Details: 15 mA | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: 5 micro-liters of sample loaded, waited 1 second,front + back blotted for 4.5 seconds at force 1 before plunging. | |||||||||
Details | This sample was monodisperse. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 90.0 K / Max: 95.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 2212 / Average exposure time: 0.985 sec. / Average electron dose: 40.0 e/Å2 Details: Images were collected at 40 frames per movie. Four movies were collected per stage shift. Frames were collected in super resolution mode at a calibrated pixel size of 0.324 A/pixel. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.1 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 136000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.15 µm / Nominal defocus min: 0.85 µm / Nominal magnification: 130000 |
Sample stage | Specimen 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
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 4-108 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 46.04 / Target criteria: Correlation coefficient |
Output model | ![]() PDB-6wkt: |