|Entry||Database: EMDB / ID: 6845|
|Title||Flagellin derivative in complex with the NLR protein NAIP5|
|Sample||Flagellin derivative in complex with NAIP5|
|Source||Mus musculus / mammal / House mouse /|
|Method||single particle reconstruction, at 4.28 Å resolution|
|Authors||Yang XR / Yang F|
|Citation||Cell Res., 2018, 28, 35-47|
|Validation Report||PDB-ID: 5yud|
SummaryFull reportAbout validation report
|Date||Deposition: Nov 21, 2017 / Header (metadata) release: Jan 3, 2018 / Map release: Jan 3, 2018 / Last update: Jan 17, 2018|
Downloads & links
|File||emd_6845.map.gz (map file in CCP4 format, 32001 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.30654 Å|
CCP4 map header:
+Entire Flagellin derivative in complex with NAIP5
|Entire||Name: Flagellin derivative in complex with NAIP5 / Number of components: 6|
+Component #1: protein, Flagellin derivative in complex with NAIP5
|Protein||Name: Flagellin derivative in complex with NAIP5 / Recombinant expression: No|
|Source||Species: Mus musculus / mammal / House mouse /|
|Source (engineered)||Expression System: Spodoptera frugiperda / arthropod / Fall armyworm|
+Component #2: protein, NAIP5
|Protein||Name: NAIP5 / Recombinant expression: No|
+Component #3: protein, Flagellin
|Protein||Name: Flagellin / Recombinant expression: No|
+Component #4: protein, Baculoviral IAP repeat-containing protein 1e
|Protein||Name: Baculoviral IAP repeat-containing protein 1e / Recombinant expression: No|
|Mass||Theoretical: 160.018047 kDa|
|Source (engineered)||Expression System: Mus musculus / mammal / House mouse /|
+Component #5: protein, Phase 2 flagellin,Flagellin
|Protein||Name: Phase 2 flagellin,Flagellin / Recombinant expression: No|
|Mass||Theoretical: 7.665362 kDa|
|Source (engineered)||Expression System: Salmonella typhimurium (strain lt2 / sgsc1412 / atcc 700720) / bacteria|
Strain: LT2 / SGSC1412 / ATCC 700720
+Component #6: ligand, ADENOSINE-5'-TRIPHOSPHATE
|Ligand||Name: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 0.507181 kDa|
|Sample solution||pH: 8|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 626608|
|3D reconstruction||Resolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution assessment)|
-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
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