|Entry||Database: PDB / ID: 5w0s|
|Title||GroEL using cryoEM|
|Descriptor||60 kDa chaperonin|
|Keywords||CHAPERONE / GroEL / cryoEM / conformational heterogeneity.|
|Specimen source||Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
|Method||Electron microscopy (3.5 Å resolution / Particle / Single particle)|
|Authors||Roh, S.H. / Chiu, W.|
|Citation||Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 8259-8264|
Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 8259-8264 Yorodumi Papers
SummaryFull reportAbout validation report
|Date||Deposition: May 31, 2017 / Release: Aug 9, 2017|
Downloads & links
A: 60 kDa chaperonin
B: 60 kDa chaperonin
C: 60 kDa chaperonin
D: 60 kDa chaperonin
E: 60 kDa chaperonin
F: 60 kDa chaperonin
G: 60 kDa chaperonin
H: 60 kDa chaperonin
I: 60 kDa chaperonin
J: 60 kDa chaperonin
K: 60 kDa chaperonin
L: 60 kDa chaperonin
M: 60 kDa chaperonin
N: 60 kDa chaperonin
Mass: 55148.020 Da / Num. of mol.: 14
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: Q6Q099
|#2: Water||ChemComp-HOH / |
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: Wild type GroEL / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Molecular weight||Value: 800 deg. / Units: KILODALTONS/NANOMETER / Experimental value: NO|
|Source (natural)||Organism: Escherichia coli|
|Source (recombinant)||Organism: Escherichia coli|
|Buffer solution||pH: 7.2|
|Specimen||Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
|Microscopy||Microscope model: JEOL 3200FSC|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD|
|Image recording||Electron dose: 1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|EM software||Name: RELION / Version: 1.4 / Category: RECONSTRUCTION|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: D7|
|3D reconstruction||Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 37367 / Symmetry type: POINT|
|Atomic model building||Details: Regarding negative occupancies: To assess fit-to-density, we derived cross-correlations at the amino acid level and by means of a map/model FSC. To perform this assessment, we generated a weighted map, derived solely from an atomic model that accounted for both ADP of all atoms and weak/negative density of all charged oxygen atoms, and compared it with the experimental map. The weighted map provides a better approximation of the experimental map by simulating map variability as opposed to treating all atoms equally. The correlations for both the FSC and the per-residue assessment showed improvements when properly weighted, further demonstrating that our model provides a good approximation of the experimental data|
-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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