|Entry||Database: EMDB / ID: 5295|
|Title||3D reconstruction of negatively stained PCSK9 in complex with a Fab|
|Sample||human PCSK9 in complex with a Fab|
|Source||Homo sapiens / human|
|Map data||3D reconstruction of negatively stained PCSK9-Fab complex|
|Method||single particle reconstruction, at 25 Å resolution|
|Authors||Wu S / Avila-Sakar A / Kim J / Booth DS / Greenberg CH / Rossi A / Liao M / Alian A / Griner SL / Juge N / Mergel CM / Chaparro-Riggers J / Strop P / Tampe R / Edwards RH / Stroud RM / Craik CS / Cheng Y|
|Citation||Structure, 2012, 20, 582-592|
Structure, 2012, 20, 582-592 Yorodumi Papers
|Date||Deposition: May 23, 2011 / Header (metadata) release: Oct 26, 2011 / Map release: May 29, 2012 / Last update: May 29, 2012|
Downloads & links
|File||emd_5295.map.gz (map file in CCP4 format, 845 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 4.26 Å|
CCP4 map header:
-Entire human PCSK9 in complex with a Fab
|Entire||Name: human PCSK9 in complex with a Fab / Number of components: 2 / Oligomeric State: monomer|
|Mass||Theoretical: 120 kDa / Experimental: 120 kDa|
-Component #1: protein, PCSK9
|Support film||200 mesh copper grid|
|Vitrification||Instrument: NONE / Cryogen name: NONE|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 20|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: each particle / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1.5 nm|
|Specimen Holder||Holder: single tilt / Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 60 deg.|
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 3876 / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Algorithm: Fourier space / Software: Frealign / CTF correction: each particle / Resolution: 25 Å / Resolution method: FSC 0.5|
-Atomic model buiding
|Modeling #1||Refinement space: REAL|
Input PDB model: 2PMW
-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