|Entry||Database: EMDB / ID: 1581|
|Title||Structure and functional role of dynein's microtubule-binding domain|
|Keywords||Assembly 1 is a helical 15 protofilaments / component name / tubulin. Assembly 2 is a monomer of the SRS-MTBD construct|
|Sample||Synthetic construct of dynein microtubule-binding domain (85-82) fused to seryl-tRNA synthase-monomer. Abbreviated name is SRS-MTBD-85-82|
|Source||Mus musculus / mammal / House Mouse / ハツカネズミ, はつかねずみ /|
|Map data||This is a 3-D map of the SRS-MTBD construct|
|Method||helical reconstruction, at 35 Å resolution|
|Authors||Carter AP / Garbarino JE / Wilson-Kubalek EM / Shipley WE / Cho C / Milligan RA / Vale RD / Gibbons IR|
|Citation||Science, 2008, 322, 1691-1695|
|Date||Deposition: Nov 5, 2008 / Header (metadata) release: Nov 7, 2008 / Map release: Jun 11, 2009 / Last update: Nov 7, 2012|
Downloads & links
|File||emd_1581.map.gz (map file in CCP4 format, 8229 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 3.5 Å|
CCP4 map header:
-Entire Synthetic construct of dynein microtubule-binding domain (85-82) ...
|Entire||Name: Synthetic construct of dynein microtubule-binding domain (85-82) fused to seryl-tRNA synthase-monomer. Abbreviated name is SRS-MTBD-85-82|
Details: The SRS-MTBD-85-82 construct has a 12 heptad long stalk, only the first 3 heptad repeats were visible in this map. No density was observed for the SRS.
Number of components: 2
Oligomeric State: SRS-MTBD-85-82 monomers bound to 15 protofilaments helical microtubules
-Component #1: protein, microtubule
|Helical parameters||Hand: RIGHT HANDED|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 4 K / Humidity: 90 % / Method: 1.5 sec blot / Details: Vitrification instrument: Vitrobot|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 29000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Energy filter: Field Emission Gun|
|Specimen Holder||Holder: eucentric / Model: GATAN LIQUID NITROGEN|
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
|Image acquisition||Number of digital images: 10 / Sampling size: 3.5 microns / Bit depth: 8|
|Processing||Method: helical reconstruction|
|3D reconstruction||Algorithm: Fourier methods / Software: phoelix / CTF correction: each image / Resolution: 35 Å / Resolution method: phase overplots|
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body / Refinement space: REAL|
Details: Protocol: Rigid body. The crystal structure was manually docked into the EM density using the chimera software package.
Input PDB model: 3ERR
Chain ID: 3ERR_A
-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