|Entry||Database: EMDB / ID: 6642|
|Title||Cryo-EM structure of the WRC-Rac1 complex|
|Keywords||cryoelectron microscopy / Wave Regulatory Complex / GTPase / actin nucleation|
|Sample||Complex of WAVE regulatory complex (WRC) and Rac1|
|Source||Homo sapiens / human|
|Map data||Reconstruction of WRC-Rac1|
|Method||single particle reconstruction, at 7 Å resolution|
|Authors||Chen B / Chou H-T / Xing W / Henry L / Walz T / Rosen MK|
|Citation||Elife, 2017, 6|
|Date||Deposition: May 3, 2016 / Header (metadata) release: Jul 13, 2016 / Map release: May 3, 2017 / Last update: May 3, 2017|
Downloads & links
|File||emd_6642.map.gz (map file in CCP4 format, 61037 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.24 Å|
CCP4 map header:
-Entire Complex of WAVE regulatory complex (WRC) and Rac1
|Entire||Name: Complex of WAVE regulatory complex (WRC) and Rac1 / Details: The sample was monodisperse. / Number of components: 2|
Oligomeric State: One heteropentamer of WRC binds to one Rac1
|Mass||Theoretical: 375 kDa|
-Component #1: protein, WAVE regulatory complex
|Protein||Name: WAVE regulatory complex / a.k.a: WRC / Oligomeric Details: heterohexamer|
Details: WRC is composed of 5 subunits: Sra1, Nap1, WAVE1, Abi2, and HSPC300.
Number of Copies: 1 / Recombinant expression: Yes
|Mass||Theoretical: 375 kDa|
|Source||Species: Homo sapiens / human|
|Source (engineered)||Expression System: Spodoptera frugiperda / arthropod / Cell of expression system: sf9|
-Component #2: protein, Rac1
|Sample solution||Specimen conc.: 0.1 mg/ml|
Buffer solution: 10 mM HEPES, 100 mM NaCl, 1 mM MgCl2, 2 mM TCEP
|Support film||glow-discharged Quantifoil holey carbon grids (400 copper mesh, R1.2/1.3)|
|Vitrification||Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 103 K / Humidity: 80 %|
Method: WRC-Rac1 complex (3.5 microliter at 0.1 mg/ml) was applied to glow-discharged Quantifoil holey carbon grids (400 copper mesh, R1.2/1.3). The grids were blotted for 3 seconds and quick-frozen in liquid ethane using a Gatan CryoPlunge 3.
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 20 / Date: Jun 16, 2015|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 38.4 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 29000 X (nominal), 40410 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 2500 nm|
|Specimen Holder||Holder: This holder operates at liquid nitrogen temperature.|
Model: OTHER / Temperature: 88 K
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 2173 / Sampling size: 5 microns|
Details: There were a total of 2,173 image stacks. For 1,366 stacks, 30 frames were recorded at 200 ms per frame (total exposure time of 6 seconds). For 407 stacks, 34 frames were recorded at 300 ms per frame (total exposure time of 10.2 seconds). For 400 stacks, 51 frames were recorded at 200 ms per frame (total exposure time of 10.2 seconds).
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 29784|
Details: Initial model was low-pass filtered crystal structure of the WRC complex (PDB ID 3P8C). Automatic particle picking, 2D classification, 3D classification, refinement, and subsequent reconstruction were performed using RELION.
|3D reconstruction||Algorithm: Cross-common lines / Software: Relion / CTF correction: whole micrograph / Resolution: 7 Å / Resolution method: FSC 0.143, gold-standard|
-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
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