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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30913 | |||||||||
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Title | 1.93 A cryo-EM structure of streptavidin | |||||||||
![]() | FSC-weighted, sharpened and masked map by PostProcess | |||||||||
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![]() | STREPTAVIDIN / CYTOSOLIC PROTEIN | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.93 Å | |||||||||
![]() | Hiraizumi M / Yamashita K / Nishizawa T / Kikkawa M / Nureki O | |||||||||
![]() | ![]() Title: 1.93 A cryo-EM structure of streptavidin Authors: Hiraizumi M | |||||||||
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 | ![]() | 1.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15 KB 15 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.1 KB | Display | ![]() |
Images | ![]() | 206.5 KB | ||
Masks | ![]() | 5.1 MB | ![]() | |
Filedesc metadata | ![]() | 5.3 KB | ||
Others | ![]() ![]() | 4.1 MB 4.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 907.5 KB | Display | ![]() |
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Full document | ![]() | 907.4 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dy0MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | FSC-weighted, sharpened and masked map by PostProcess | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8 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 | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_30913_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_30913_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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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: ![]() |
-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: ![]() |
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 |
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.2 |
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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 |
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Electron microscopy
Microscope | TFS KRIOS |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |