|Entry||Database: PDB / ID: 5vt0|
|Title||Escherichia coli 6S RNA derivative in complex with Escherichia coli RNA polymerase sigma70-holoenzyme|
|Descriptor||Escherichia coli sigma 70 (rpoD)/RNA Complex|
(Escherichia coli RNA polymerase ...) x 4
|Keywords||transcription/RNA / RNAP / 6S RNA / ncRNA / transcription regulation / transcription-RNA complex|
|Specimen source||Escherichia coli (strain k12) / bacteria / |
Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
|Method||Electron microscopy (3.78 Å resolution / Particle / Single particle)|
|Authors||Chen, J. / Darst, S.A.|
|Citation||Mol. Cell, 2017, 68, 388-397.e6|
SummaryFull reportAbout validation report
|Date||Deposition: May 15, 2017 / Release: Nov 1, 2017|
Downloads & links
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
R: Escherichia coli 6S RNA derivative (112-MER)
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules G
H I J K
Mass: 26330.996 Da / Num. of mol.: 2 / Source: (gene. exp.) Escherichia coli (strain K12) / References: UniProt: P0A7Z4, EC: 18.104.22.168
Mass: 150820.875 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (strain K12) / References: UniProt: P0A8V2, EC: 22.214.171.124
Mass: 155366.781 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (strain K12) / References: UniProt: P0A8T7, EC: 126.96.36.199
-Polypeptide(L) / RNA chain , 2 types, 2 molecules L
Mass: 60464.371 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (strain K12) / References: UniProt: P00579
|#6: RNA chain|
Mass: 46308.500 Da / Num. of mol.: 1 / Details: prepared by in vitro transcription / Source: (synth.) Escherichia coli
-Non-polymers , 2 types, 3 molecules
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: Escherichia coli 6S RNA derivative in complex with Escherichia coli RNA polymerase sigma70-holoenzyme|
Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6 / Source: RECOMBINANT
|Molecular weight||Value: 0.475 deg. / Units: MEGADALTONS / Experimental value: YES|
|Source (natural)||Organism: Escherichia coli|
|Source (recombinant)||Organism: Escherichia coli BL21(DE3)|
|Buffer solution||pH: 8|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD|
|Image recording||Electron dose: 1.8 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|Software||Name: PHENIX / Version: 1.12_2829: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 362926 / Symmetry type: POINT|
|Atomic model building||Ref protocol: OTHER / Ref space: REAL / Target criteria: Correlation coefficient|
|Least-squares process||Highest resolution: 3.78 Å|
|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.
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- 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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