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- EMDB-0689: The reconstruction of biotin-bound streptavidin at 3.2 Angstrom r... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0689 | |||||||||
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Title | The reconstruction of biotin-bound streptavidin at 3.2 Angstrom resolution | |||||||||
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![]() | streptavidin / CYTOSOLIC PROTEIN | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Fan X / Wang J / Lei JL / Wang HW | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.5 KB 13.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 4.6 KB | Display | ![]() |
Images | ![]() | 115.1 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j6jMC ![]() 0690C ![]() 6j6kC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 5.5 TB Data #1: Uncorrected biotinbound state streptavidin movie stacks, binning 2 from super-resolution stacks. [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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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: ![]() |
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: ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |