+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30913 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 1.93 A cryo-EM structure of streptavidin | |||||||||
Map data | FSC-weighted, sharpened and masked map by PostProcess | |||||||||
Sample |
| |||||||||
Keywords | STREPTAVIDIN / CYTOSOLIC PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces avidinii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.93 Å | |||||||||
Authors | Hiraizumi M / Yamashita K / Nishizawa T / Kikkawa M / Nureki O | |||||||||
Citation | Journal: To Be Published Title: 1.93 A cryo-EM structure of streptavidin Authors: Hiraizumi M | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30913.map.gz | 1.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-30913-v30.xml emd-30913.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30913_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_30913.png | 206.5 KB | ||
Masks | emd_30913_msk_1.map | 5.1 MB | Mask map | |
Filedesc metadata | emd-30913.cif.gz | 5.3 KB | ||
Others | emd_30913_half_map_1.map.gz emd_30913_half_map_2.map.gz | 4.1 MB 4.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30913 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30913 | HTTPS FTP |
-Validation report
Summary document | emd_30913_validation.pdf.gz | 907.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_30913_full_validation.pdf.gz | 907.4 KB | Display | |
Data in XML | emd_30913_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | emd_30913_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30913 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30913 | HTTPS FTP |
-Related structure data
Related structure data | 7dy0MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10641 (Title: 1.93 A cryo-EM structure of streptavidin / Data size: 373.1 / Data #1: Unaligned movies [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_30913.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | FSC-weighted, sharpened and masked map by PostProcess | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_30913_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_30913_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_30913_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Streptavidin
Entire | Name: Streptavidin |
---|---|
Components |
|
-Supramolecule #1: Streptavidin
Supramolecule | Name: Streptavidin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Streptomyces avidinii (bacteria) |
-Macromolecule #1: Streptavidin
Macromolecule | Name: Streptavidin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
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: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 30 / Formula: HOH |
---|---|
Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
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 / Details: coated grid with pentylamine before glow discharge |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2277 / Average exposure time: 1.5 sec. / 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 |