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Yorodumi- EMDB-0689: The reconstruction of biotin-bound streptavidin at 3.2 Angstrom r... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0689 | |||||||||
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Title | The reconstruction of biotin-bound streptavidin at 3.2 Angstrom resolution | |||||||||
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: 3.2 Å | |||||||||
Authors | Fan X / Wang J / Lei JL / Wang HW | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution. Authors: Xiao Fan / Jia Wang / Xing Zhang / Zi Yang / Jin-Can Zhang / Lingyun Zhao / Hai-Lin Peng / Jianlin Lei / Hong-Wei Wang / Abstract: The fast development of single-particle cryogenic electron microscopy (cryo-EM) has made it more feasible to obtain the 3D structure of well-behaved macromolecules with a molecular weight higher than ...The fast development of single-particle cryogenic electron microscopy (cryo-EM) has made it more feasible to obtain the 3D structure of well-behaved macromolecules with a molecular weight higher than 300 kDa at ~3 Å resolution. However, it remains a challenge to obtain the high-resolution structures of molecules smaller than 200 kDa using single-particle cryo-EM. In this work, we apply the Cs-corrector-VPP-coupled cryo-EM to study the 52 kDa streptavidin (SA) protein supported on a thin layer of graphene and embedded in vitreous ice. We are able to solve both the apo-SA and biotin-bound SA structures at near-atomic resolution using single-particle cryo-EM. We demonstrate that the method has the potential to determine the structures of molecules as small as 39 kDa. | |||||||||
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_0689.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-0689-v30.xml emd-0689.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0689_fsc.xml | 4.6 KB | Display | FSC data file |
Images | emd_0689.png | 115.1 KB | ||
Filedesc metadata | emd-0689.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0689 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0689 | HTTPS FTP |
-Validation report
Summary document | emd_0689_validation.pdf.gz | 399 KB | Display | EMDB validaton report |
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Full document | emd_0689_full_validation.pdf.gz | 398.6 KB | Display | |
Data in XML | emd_0689_validation.xml.gz | 8 KB | Display | |
Data in CIF | emd_0689_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0689 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0689 | HTTPS FTP |
-Related structure data
Related structure data | 6j6jMC 0690C 6j6kC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10270 (Title: Single particle reconstruction of 52 kDa biotin-bound state streptavidin at 3.2 Angstrom resolution Data size: 5.5 TB Data #1: Uncorrected biotinbound state streptavidin movie stacks, binning 2 from super-resolution stacks. [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0689.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.053 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Streptavidin with biotin
Entire | Name: Streptavidin with biotin |
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Components |
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-Supramolecule #1: Streptavidin with biotin
Supramolecule | Name: Streptavidin with biotin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Streptomyces avidinii (bacteria) |
Molecular weight | Theoretical: 52 KDa |
-Macromolecule #1: Streptavidin
Macromolecule | Name: Streptavidin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Streptomyces avidinii (bacteria) |
Molecular weight | Theoretical: 12.596641 KDa |
Sequence | String: GITGTWYNQL GSTFIVTAGA DGALTGTYES AVGNAESRYV LTGRYDSAPA TDGSGTALGW TVAWKNNYRN AHSATTWSGQ YVGGAEARI NTQWLLTSGT TEANAWKSTL VGHDTFTKVK UniProtKB: Streptavidin |
-Macromolecule #2: BIOTIN
Macromolecule | Name: BIOTIN / type: ligand / ID: 2 / Number of copies: 4 / 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: 12 / 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 | 0.2 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE Spherical aberration corrector: spherical aberration corrector |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 1450 / Average exposure time: 2.56 sec. / Average electron dose: 50.0 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: 0.01 mm / Nominal defocus max: -0.8 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 215000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |