|Entry||Database: EMDB / ID: 6067|
|Title||Negative stain EM structure of the yeast dynein motor domain with stalk and MTBD in the presence of ATP|
|Map data||Reconstruction of yeast dynein motor domain with full stalk and MTBD in the presence of 5 mM ATP|
|Sample||yeast dynein motor domain with full stalk and MTBD in the presence of 5 mM ATP:|
|Keywords||motor proteins / power stroke / dynein / AAA protein / ATPase|
|Function / homology||Dynein heavy chain, N-terminal region 1 / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, domain-1 / Dynein heavy chain, domain-2 / Dynein heavy chain, AAA module D4 / Dynein heavy chain, N-terminal region 2 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / P-loop containing nucleoside triphosphate hydrolase / Dynein heavy chain, hydrolytic ATP-binding dynein motor region ...Dynein heavy chain, N-terminal region 1 / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, domain-1 / Dynein heavy chain, domain-2 / Dynein heavy chain, AAA module D4 / Dynein heavy chain, N-terminal region 2 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / P-loop containing nucleoside triphosphate hydrolase / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain region D6 P-loop domain / ATP-binding dynein motor region / AAA+ ATPase domain / karyogamy / astral microtubule / nuclear migration along microtubule / minus-end-directed vesicle transport along microtubule / establishment of mitotic spindle localization / dynein light chain binding / ATP-dependent microtubule motor activity, minus-end-directed / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein complex / dynein intermediate chain binding / spindle pole body / establishment of mitotic spindle orientation / cytoplasmic microtubule organization / mitotic sister chromatid segregation / cytoplasmic microtubule / microtubule-based movement / cell cortex / ATP binding / Dynein heavy chain, cytoplasmic|
Function and homology information
|Source||Saccharomyces cerevisiae (baker's yeast)|
|Method||single particle reconstruction / negative staining / 23 Å resolution|
|Authors||Bhabha G / Moeller A / Liao M / Speir JA / Vale RD / Cheng Y|
|Citation||Journal: Cell / Year: 2014|
Title: Allosteric communication in the dynein motor domain.
Authors: Gira Bhabha / Hui-Chun Cheng / Nan Zhang / Arne Moeller / Maofu Liao / Jeffrey A Speir / Yifan Cheng / Ronald D Vale
|Date||Deposition: Aug 27, 2014 / Header (metadata) release: Sep 24, 2014 / Map release: Nov 5, 2014 / Last update: Dec 17, 2014|
|Structure viewer||EM map: |
Downloads & links
|File||emd_6067.map.gz (map file in CCP4 format, 1025 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 4.26 Å|
CCP4 map header:
-Entire yeast dynein motor domain with full stalk and MTBD in the presenc...
|Entire||Name: yeast dynein motor domain with full stalk and MTBD in the presence of 5 mM ATP|
Number of components: 1 / Oligomeric State: monomer
|Mass||Theoretical: 303 kDa|
-Component #1: protein, dynein
|Protein||Name: dynein / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 1|
|Mass||Theoretical: 303 kDa|
|Source||Species: Saccharomyces cerevisiae (baker's yeast) / Strain: VY137|
|Source (engineered)||Expression System: Saccharomyces cerevisiae (baker's yeast)|
|External references||UniProt: Dynein heavy chain, cytoplasmic|
|Specimen||Specimen state: particle / Method: negative staining|
|Sample solution||Specimen conc.: 0.02 mg/ml|
Buffer solution: 50 mM Tris, pH 8.0, 200 mM sodium chloride, 1 mM EGTA, 2 mM magnesium acetate, 1 mM DTT
|Support film||Cu 400 mesh|
|Staining||Samples were applied to freshly glow discharged carbon coated grids and blotted off. Immediately after blotting, a 2% uranyl formate solution was applied for staining and blotted off. The stain was applied five times per sample. Samples were allowed to air dry before imaging.|
|Vitrification||Instrument: NONE / Cryogen name: NONE|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Feb 27, 2013|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 80000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3500 nm|
|Specimen Holder||Model: SIDE ENTRY, EUCENTRIC|
|Camera||Detector: TVIPS TEMCAM-F416 (4k x 4k)|
|Image acquisition||Number of digital images: 168|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 1827|
|3D reconstruction||Software: Relion / Resolution: 23 Å / Resolution method: FSC 0.143, gold-standard|
-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
+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
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