|Entry||Database: EMDB / ID: 3805|
|Title||Cryo-EM structure of jasplakinolide-stabilized malaria parasite F-actin at near-atomic resolution|
|Sample||Plasmodium falciparum actin 1 filament stabilized by jasplakinolide|
|Source||Plasmodium falciparum hb3 / eukaryote / image: Plasmodium falciparum|
|Method||single particle reconstruction, at 3.8 Å resolution|
|Authors||Pospich S / Kumpula E-P|
|Citation||Proc. Natl. Acad. Sci. U.S.A., 2017|
|Validation Report||PDB-ID: 5ogw|
SummaryFull reportAbout validation report
|Date||Deposition: Jul 13, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Sep 27, 2017 / Last update: Sep 27, 2017|
Downloads & links
|File||emd_3805.map.gz (map file in CCP4 format, 67109 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.14 Å|
CCP4 map header:
|File||emd_3805_msk_1.map ( map file in CCP4 format, 67109 KB )|
|Projections & Slices|
|Data type||Image stored as Reals|
|Space group number||1|
+Entire Plasmodium falciparum actin 1 filament stabilized by jasplakinolide
|Entire||Name: Plasmodium falciparum actin 1 filament stabilized by jasplakinolide|
Details: Filament / Number of components: 5
+Component #1: protein, Plasmodium falciparum actin 1 filament stabilized by jas...
|Protein||Name: Plasmodium falciparum actin 1 filament stabilized by jasplakinolide|
Details: Filament / Recombinant expression: No
|Source||Species: Plasmodium falciparum hb3 / eukaryote / image: Plasmodium falciparum|
|Source (engineered)||Expression System: Spodoptera frugiperda / arthropod|
+Component #2: protein, Actin-1
|Protein||Name: Actin-1 / Recombinant expression: No|
|Mass||Theoretical: 42.047676 kDa|
|Source (engineered)||Expression System: Plasmodium falciparum (isolate hb3) / eukaryote / |
Strain: isolate HB3
+Component #3: ligand, ADENOSINE-5'-DIPHOSPHATE
|Ligand||Name: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 5 / Recombinant expression: No|
|Mass||Theoretical: 0.427201 kDa|
+Component #4: ligand, MAGNESIUM ION
|Ligand||Name: MAGNESIUM ION / Number of Copies: 5 / Recombinant expression: No|
|Mass||Theoretical: 2.430505 MDa|
+Component #5: ligand, Jasplakinolide
|Ligand||Name: Jasplakinolide / Number of Copies: 3 / Recombinant expression: No|
|Mass||Theoretical: 0.70967 kDa|
|Sample solution||Buffer solution: 10 mM HEPES pH 7.5, 0.2 mM CaCl2, 50 mM KCl, 4 mM MgCl2, 5 mM DTT and 0.5 mM ATP. JAS was added at a 1:1 molar ratio during polyermization.|
|Vitrification||Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 97 %|
Details: Sample (2 uL of JAS-stabilized F-actin solution) was applied to a glow-discharged holey carbon grid, incubated for 30 s and manually blotted for 4 s from the backside with filter paper.
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Details: Cs corrected microscope|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 110 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Imaging mode: BRIGHT FIELD / Defocus: 800 - 2700 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Image acquisition||Number of digital images: 1634|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 140716|
|3D reconstruction||Software: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
-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
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+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
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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
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Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
Thousand views of thousand structures
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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