|Entry||Database: PDB / ID: 6b7y|
|Title||Cryo-EM structure of human insulin degrading enzyme|
|Descriptor||Insulin-degrading enzyme (E.C.126.96.36.199)|
|Keywords||HYDROLASE / IDE / insulin degrading enzyme / amyloid beta / BIOSYNTHETIC PROTEIN|
|Specimen source||Homo sapiens / human|
|Method||Electron microscopy (6.5 Å resolution / Particle / Single particle)|
|Authors||Liang, W.G. / Zhang, Z. / Bailey, L.J. / Kossiakoff, A.A. / Tan, Y.Z. / Wei, H. / Carragher, B. / Potter, S.C. / Tang, W.J.|
|Citation||To Be Published|
To Be Published Search PubMed
SummaryFull reportAbout validation report
|Date||Deposition: Oct 5, 2017 / Release: Nov 8, 2017|
Downloads & links
A: Insulin-degrading enzyme
B: Insulin-degrading enzyme
Mass: 111866.484 Da / Num. of mol.: 2 / Fragment: residues 46-1011 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P14735, EC: 188.8.131.52
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: Insulin degrading enzyme / Type: COMPLEX|
Details: Cryo-EM structure of human Apo insulin degrading enzyme
Entity ID: 1 / Source: RECOMBINANT
|Molecular weight||Value: 0.1 deg. / Units: MEGADALTONS / Experimental value: YES|
|Source (natural)||Organism: Homo sapiens|
|Source (recombinant)||Organism: Escherichia coli / Strain: BL|
|Buffer solution||pH: 7.8|
|Specimen||Conc.: 0.3 mg/ml / Details: The sample was monodisperse / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: The grids are homemade lacey gold nanowire grids / Grid material: GOLD / Grid mesh size: 300 / Grid type: Homemade|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 298 kelvins / Details: The cryo grids were made using Spotiton|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS / Details: The image was collected at 20-50 degree tilt|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 22500 / Calibrated magnification: 46598 / Nominal defocus max: 2200 nm / Nominal defocus min: 940 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 kelvins / Temperature (min): 70 kelvins / Residual tilt: 10 mradians|
Imaging ID: 1 / Average exposure time: 10 sec. / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1
|Image scans||Sampling size: 5 microns / Dimension width: 3710 / Dimension height: 3838 / Movie frames/image: 50 / Used frames/image: 1-50|
|Software||Name: PHENIX / Version: 1.12_2829: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Number of particles selected: 762283|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 24425 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT|
|Atomic model building||Overall b value: 92 / Ref protocol: FLEXIBLE FIT / Ref space: REAL|
|Refine LS restraints|
-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
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