|Entry||Database: EMDB / ID: 5890|
|Title||Cryo-EM structure of MAVS CARD filament|
|Keywords||Innate immunity / helical filament|
|Sample||MAVS CARD filament|
|Source||Homo sapiens / human|
|Map data||Cryo-EM map of MAVS CARD filament|
|Method||helical reconstruction, at 9.6 Å resolution|
|Authors||Xu H / He X / Zheng H / Huang LJ / Hou F / Yu Z / de la Cruz MJ / Borkowski B / Zhang X / Chen ZJ / Jiang Q-X|
|Citation||Elife, 2014, 3, e01489-e01489|
Elife, 2014, 3, e01489-e01489 Yorodumi Papers
|Validation Report||PDB-ID: 3j6c|
SummaryFull reportAbout validation report
|Date||Deposition: Jan 22, 2014 / Header (metadata) release: Feb 19, 2014 / Map release: Mar 5, 2014 / Last update: Oct 7, 2015|
Downloads & links
|File||emd_5890.map.gz (map file in CCP4 format, 978 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.333 Å|
CCP4 map header:
-Entire MAVS CARD filament
|Entire||Name: MAVS CARD filament / Number of components: 1 / Oligomeric State: polymer|
|Mass||Theoretical: 546 kDa|
-Component #1: protein, Mitochondrial antiviral-signaling protein (MAVS)
|Protein||Name: Mitochondrial antiviral-signaling protein (MAVS) / a.k.a: IPS1, KIAA1271, VISA / Oligomeric Details: polymer / Recombinant expression: Yes|
|Mass||Theoretical: 13 kDa|
|Source||Species: Homo sapiens / human|
|Source (engineered)||Expression System: Homo sapiens / human / Vector: pcDNA3 / Cell of expression system: HEK293T|
|External references||UniProt: UniProt: Q7Z434|
|Helical parameters||Axial symmetry: C3 (3 fold cyclic) / Hand: LEFT HANDED / Delta z: 16.8 Å / Delta phi: 53.6 deg.|
|Sample solution||Buffer solution: 20mM Tris-HCl, 50mM NaCl, 1mM DTT / pH: 7.5|
|Support film||Quantifoil grids coated with thin carbon on top|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 2200FS / Date: Oct 20, 2011|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 60000 X (nominal), 61950 X (calibrated)|
Astigmatism: Objective lens astigmatism was corrected at 100,000x magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2000 nm / Energy filter: JEOL omega filter / Energy window: 0-35 eV
|Specimen Holder||Model: GATAN LIQUID NITROGEN|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Scanner: ZEISS SCAI / Sampling size: 7 microns / URL of raw data: http://dx.doi.org/10.6019/EMPIAR-10014|
|Raw data||EMPIAR-10014 (Title: MAVS CARD and DeltaProTM filaments / Data size: 35.3 GB / Data #1: CARD set1 micrographs [micrographs - single frame] / Data #2: CARD set2 micrographs [micrographs - single frame] / Data #3: CARD set3 micrographs [micrographs - single frame] / Data #4: CARD set4 micrographs [micrographs - single frame]|
Data #5: CARD set1 segments [picked particles - single frame - unprocessed]
Data #6: CARD set2 segments [picked particles - single frame - unprocessed]
Data #7: CARD set3 segments [picked particles - single frame - unprocessed]
Data #8: CARD set4 segments [picked particles - single frame - unprocessed]
Data #9: DeltProTM micrographs [micrographs - single frame]
Data #10: DeltaProTM segments [picked particles - single frame - unprocessed])
|Processing||Method: helical reconstruction / Details: IHRSR|
|3D reconstruction||Algorithm: IHRSR / Software: Spider, MRC, EMAN, IMAGIC4D / CTF correction: Each filament segment|
Details: Final data were calculated from three separate datasets from three sessions of data collection. The handedness of the map was determined by cryo-electron tomography.
Resolution: 9.6 Å / Resolution method: FSC 0.5, gold-standard
-Atomic model buiding
|Modeling #1||Software: Chimera, SITUS / Refinement protocol: rigid body / Refinement space: REAL|
Details: The docking of one X-ray model into a segmented map corresponding to one subunit was first done manually in Chimera, and then optimized using SITUS.
Input PDB model: 2VGQ
Chain ID: 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
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