|Entry||Database: PDB / ID: 3lue|
|Title||Model of alpha-actinin CH1 bound to F-actin|
|Descriptor||Actin, cytoplasmic 1, Alpha-actinin-3|
|Keywords||STRUCTURAL PROTEIN / calponin homology domains / Acetylation / ATP-binding / Cytoplasm / Cytoskeleton / Methylation / Nucleotide-binding / Phosphoprotein / Actin-binding / Calcium / Polymorphism / Deafness / Disease mutation / Dystonia|
|Specimen source||Homo sapiens / human|
|Method||Electron microscopy (15 Å resolution / Filament / Helical)|
|Authors||Galkin, V.E. / Orlova, A. / Salmazo, A. / Djinovic-Carugo, K. / Egelman, E.H.|
|Citation||Nat. Struct. Mol. Biol., 2010, 17, 614-616|
SummaryFull reportAbout validation report
|Date||Deposition: Feb 17, 2010 / Release: Apr 28, 2010|
Downloads & links
A: Actin, cytoplasmic 1
B: Actin, cytoplasmic 1
C: Actin, cytoplasmic 1
D: Actin, cytoplasmic 1
E: Actin, cytoplasmic 1
F: Actin, cytoplasmic 1
G: Actin, cytoplasmic 1
H: Actin, cytoplasmic 1
I: Actin, cytoplasmic 1
J: Actin, cytoplasmic 1
|Details||Authors state that the model is from a continuous helix where the rotation per subunit is -167.2 degrees and the rise per subunit is 26.6 Angstroms.|
Mass: 41651.465 Da / Num. of mol.: 10 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P60709
Mass: 12471.712 Da / Num. of mol.: 10 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: Q08043
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / Reconstruction method: HELICAL|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 50000 / Camera length: 0 mm|
|Specimen holder||Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: gatan 626 / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.|
|Image recording||Film or detector model: KODAK SO-163 FILM|
|Image scans||Sampling size: 12.7 microns / Scanner model: NIKON COOLSCAN|
|CTF correction||Details: Weiner filter|
|Helical symmerty||Angular rotation/subunit: 166.8 deg. / Axial rise/subunit: 27.7 Å / Axial symmetry: C1|
|3D reconstruction||Method: back projection / Resolution: 15 Å / Resolution method: FSC 0.5 CUT-OFF / Nominal pixel size: 2.38 / Actual pixel size: 2.38|
Details: AUTHORS STATE THAT THE STRANGE C-N BONDS WERE THE RESULT OF BREAKING THE CHAINS AT THESE POINTS TO DO RIGID BODY FITTING OF THE SUBDOMAINS.
Symmetry type: HELICAL
|Atomic model building||Details: METHOD--both manually and with Chimera DETAILS--AUTHORS STATE THAT THE STRANGE C-N BONDS WERE THE RESULT OF BREAKING THE CHAINS AT THESE POINTS TO DO RIGID BODY FITTING OF THE SUBDOMAINS.|
Ref protocol: OTHER / Ref space: REAL
|Number of atoms included #LAST||Protein: 37910 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 37910|
-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