|Entry||Database: EMDB / ID: EMD-0689|
|Title||The reconstruction of biotin-bound streptavidin at 3.2 Angstrom resolution|
|Sample||Streptavidin with biotin:|
Streptavidin / (ligand) x 2
|Function / homology||Avidin/streptavidin / Avidin / Avidin-like, conserved site / Avidin-like superfamily / biotin binding / extracellular region / Streptavidin|
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 |
|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.
|Validation Report||PDB-ID: 6j6j|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_0689.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.053 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Streptavidin with biotin
|Entire||Name: Streptavidin with biotin / Number of components: 4|
-Component #1: protein, Streptavidin with biotin
|Protein||Name: Streptavidin with biotin / Recombinant expression: No|
|Mass||Experimental: 52 kDa|
|Source||Species: Streptomyces avidinii (bacteria)|
-Component #2: protein, Streptavidin
|Protein||Name: Streptavidin / Number of Copies: 4 / Recombinant expression: No|
|Mass||Theoretical: 12.596641 kDa|
|Source||Species: Streptomyces avidinii (bacteria)|
-Component #3: ligand, BIOTIN
|Ligand||Name: BIOTIN / Number of Copies: 4 / Recombinant expression: No|
|Mass||Theoretical: 0.244311 kDa|
-Component #4: ligand, water
|Ligand||Name: water / Number of Copies: 12 / Recombinant expression: No|
|Mass||Theoretical: 1.801505 MDa|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.2 mg/mL / pH: 7.5|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 285 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 215000.0 X (nominal) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: -800.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 1450 / Sampling size: 5 µm|
|Processing||Method: single particle reconstruction / Applied symmetry: D2 (2x2 fold dihedral) / Number of projections: 45686|
|3D reconstruction||Software: RELION / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution estimation)|
-Atomic model buiding
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.:Changes in new EM Navigator and Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi