|Entry||Database: PDB / ID: 6j6j|
|Keywords||CYTOSOLIC PROTEIN / streptavidin|
|Function / homology|
Function and homology information
biotin binding / extracellular region
Avidin/streptavidin / Avidin / Avidin-like, conserved site / Avidin-like superfamily / Avidin family / Avidin-like / Lipocalin / Beta Barrel / Mainly Beta
|Biological species||Streptomyces avidinii (bacteria)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å|
|Authors||Fan, X. / Wang, J. / Lei, J.L. / Wang, H.W.|
|Funding support|| China, 1items |
|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.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
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Mass: 12596.641 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
|#3: Water|| ChemComp-HOH / |
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Streptavidin with biotin / Type: COMPLEX / Entity ID: 1 / Source: NATURAL|
|Molecular weight||Value: 0.052 MDa / Experimental value: YES|
|Source (natural)||Organism: Streptomyces avidinii (bacteria)|
|Buffer solution||pH: 7.5|
|Specimen||Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285 K|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 215000 X / Nominal defocus max: -800 nm / Nominal defocus min: -800 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU|
|Specimen holder||Cryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 2.56 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1450|
|EM imaging optics||Phase plate: Using volta phase plate|
Spherical aberration corrector: Using spherical aberration corrector
|Image scans||Sampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 32 / Used frames/image: 1-32|
|Software||Name: PHENIX / Version: 1.14_3260: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Num. of particles selected: 1346980|
|Symmetry||Point symmetry: D2 (2x2 fold dihedral)|
|3D reconstruction||Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45686 / Num. of class averages: 1 / Symmetry type: POINT|
|Refine LS restraints|
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