|Entry||Database: EMDB / ID: 1059|
|Title||Electron cryomicroscopy structure of N-ethyl maleimide sensitive factor at 11 A resolution.|
|Sample||NSF alpha-SNAP SNARE 20S|
|Source||Cricetulus griseus / mammal / Chinese Hamster / モンゴルキヌゲネズミ|
Bos taurus / mammal / Cattle / ウシ /
Unidentified / Chinese Hamster
|Map data||3D density map of NSF?alpha-SNAP?SNARE (20S)|
|Method||single particle reconstruction, at 11 Å resolution|
|Authors||Furst J / Sutton RB / Chen J / Brunger AT / Grigorieff N|
|Citation||EMBO J., 2003, 22, 4365-4374|
|Date||Deposition: Oct 10, 2003 / Header (metadata) release: Oct 10, 2003 / Map release: Oct 10, 2003 / Last update: Oct 24, 2012|
Downloads & links
|File||emd_1059.map.gz (map file in CCP4 format, 2849 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 3.5 Å|
CCP4 map header:
-Entire NSF alpha-SNAP SNARE 20S
|Entire||Name: NSF alpha-SNAP SNARE 20S|
Details: The sample was monodisperse. Some domains were disordered.
Number of components: 3
|Mass||Experimental: 680 kDa / Measured by: gel permeation chromatography|
-Component #1: protein, N-ethyl Maleimide Sensitive Factor
|Protein||Name: N-ethyl Maleimide Sensitive Factor / a.k.a: NSF / Oligomeric Details: hexamer / Details: 6 subunits / Number of Copies: 6 / Recombinant expression: Yes|
|Mass||Experimental: 82.8 kDa|
|Source||Species: Cricetulus griseus / mammal / Chinese Hamster / モンゴルキヌゲネズミ|
|Source (engineered)||Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
-Component #2: protein, Soluble NSF Attachment Protein
|Protein||Name: Soluble NSF Attachment Protein / a.k.a: alpha-SNAP / Recombinant expression: Yes|
|Mass||Experimental: 33.4 kDa|
|Source||Species: Bos taurus / mammal / Cattle / ウシ /|
-Component #3: protein, Soluble NSF Attachment Protein Receptor
|Protein||Name: Soluble NSF Attachment Protein Receptor / a.k.a: SNARE / Recombinant expression: Yes|
|Mass||Experimental: 82.3 kDa|
|Source||Species: Unidentified / Chinese Hamster|
|Sample solution||Specimen conc.: 0.2 mg/ml|
Buffer solution: 20mM HEPES, pH 7.4, 300 mM NACl, 2 mM MgCl2, 5mM b-mercaptoethanol, 0.01/0.1 mM ADP/ATP nucleotide
|Support film||holey carbon film|
|Staining||cryo (no stain)|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 85 K / Humidity: 80 % / Details: Vitrification instrument: Technion plunger|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 62000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4000 nm|
|Specimen Holder||Holder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 85 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / OD range: 1.4 / Details: 3 x 3 averaging, final step size = 27 microns|
|Processing||Method: single particle reconstruction / Number of projections: 31592 / Details: manual particle selection / Applied symmetry: C6 (6 fold cyclic)|
|3D reconstruction||Algorithm: Common lines / Software: IMAGIC, FREALIGN / CTF correction: FREALIGN / Resolution: 11 Å / Resolution method: FSC 0.5 / Details: Final map was calculated from three data sets|
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
-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 / EM Navigator (legacy version) / Yorodumi (legacy version)
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi