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Yorodumi- EMDB-31084: 1.77 A cryo-EM structure of Streptavidin using first 40 frames (c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31084 | |||||||||
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Title | 1.77 A cryo-EM structure of Streptavidin using first 40 frames (corresponding to about 40 e/A^2 total dose) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | STREPTAVIDIN / CYTOSOLIC PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces avidinii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.77 Å | |||||||||
Authors | Hiraizumi M / Yamashita K / Nishizawa T / Kotecha A / Nureki O | |||||||||
Citation | Journal: To Be Published Title: 1.77 A cryo-EM structure of Streptavidin using first 40 frames (corresponding to about 40e/A^2 total dose) Authors: Hiraizumi M | |||||||||
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_31084.map.gz | 2.1 MB | EMDB map data format | |
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Header (meta data) | emd-31084-v30.xml emd-31084.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31084_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_31084.png | 180.1 KB | ||
Masks | emd_31084_msk_1.map | 12.9 MB | Mask map | |
Filedesc metadata | emd-31084.cif.gz | 5 KB | ||
Others | emd_31084_half_map_1.map.gz emd_31084_half_map_2.map.gz | 11.1 MB 11.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31084 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31084 | HTTPS FTP |
-Validation report
Summary document | emd_31084_validation.pdf.gz | 810.3 KB | Display | EMDB validaton report |
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Full document | emd_31084_full_validation.pdf.gz | 809.9 KB | Display | |
Data in XML | emd_31084_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | emd_31084_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31084 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31084 | HTTPS FTP |
-Related structure data
Related structure data | 7efdMC 7efcC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31084.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.74034 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_31084_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_31084_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31084_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Streptavidin
Entire | Name: Streptavidin |
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Components |
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-Supramolecule #1: Streptavidin
Supramolecule | Name: Streptavidin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Streptomyces avidinii (bacteria) |
-Macromolecule #1: Streptavidin
Macromolecule | Name: Streptavidin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Streptomyces avidinii (bacteria) |
Molecular weight | Theoretical: 18.849672 KDa |
Sequence | String: MRKIVVAAIA VSLTTVSITA SASADPSKDS KAQVSAAEAG ITGTWYNQLG STFIVTAGAD GALTGTYESA VGNAESRYVL TGRYDSAPA TDGSGTALGW TVAWKNNYRN AHSATTWSGQ YVGGAEARIN TQWLLTSGTT EANAWKSTLV GHDTFTKVKP S AASIDAAK KAGVNNGNPL DAVQQ UniProtKB: Streptavidin |
-Macromolecule #2: BIOTIN
Macromolecule | Name: BIOTIN / type: ligand / ID: 2 / Number of copies: 1 / Formula: BTN |
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Molecular weight | Theoretical: 244.311 Da |
Chemical component information | ChemComp-BTN: |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 39 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.2 |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 4053 / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: RECIPROCAL | ||||||
Output model | PDB-7efd: |