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- PDB-6gh5: Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gh5 | |||||||||||||||||||||
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Title | Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme transcription open complex | |||||||||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Specimen source | ![]() ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Glyde, R. / Ye, F.Z. / Zhang, X.D. | |||||||||||||||||||||
![]() | Journal: Mol. Cell / Year: 2018 Title: Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation. ![]() Abstract: Gene transcription is carried out by multi-subunit RNA polymerases (RNAPs). Transcription initiation is a dynamic multi-step process that involves the opening of the double-stranded DNA to form a ...Gene transcription is carried out by multi-subunit RNA polymerases (RNAPs). Transcription initiation is a dynamic multi-step process that involves the opening of the double-stranded DNA to form a transcription bubble and delivery of the template strand deep into the RNAP for RNA synthesis. Applying cryoelectron microscopy to a unique transcription system using σ (σ), the major bacterial variant sigma factor, we capture a new intermediate state at 4.1 Å where promoter DNA is caught at the entrance of the RNAP cleft. Combining with new structures of the open promoter complex and an initial de novo transcribing complex at 3.4 and 3.7 Å, respectively, our studies reveal the dynamics of DNA loading and mechanism of transcription bubble stabilization that involves coordinated, large-scale conformational changes of the universally conserved features within RNAP and DNA. In addition, our studies reveal a novel mechanism of strand separation by σ. | |||||||||||||||||||||
Validation Report | ![]() ![]() ![]() | |||||||||||||||||||||
Date | Deposition: May 4, 2018 / Release: Jul 4, 2018
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmcif format | ![]() ![]() |
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Links
-Related structure data
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Assembly
Deposited unit | ![]()
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein/peptide | ![]() Mass: 36558.680 Da / Num. of mol.: 2 Source: (gene. exp.) ![]() ![]() ![]() Gene: rpoA, pez, phs, sez, b3295, JW3257 Production host: ![]() ![]() ![]() References: UniProt: P0A7Z4, ![]() #2: Protein/peptide | | ![]() Mass: 150820.875 Da / Num. of mol.: 1 Source: (gene. exp.) ![]() ![]() ![]() Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 Production host: ![]() ![]() ![]() References: UniProt: P0A8V2, ![]() #3: Protein/peptide | | ![]() Mass: 155366.781 Da / Num. of mol.: 1 Source: (gene. exp.) ![]() ![]() ![]() Gene: rpoC, tabB, b3988, JW3951 Production host: ![]() ![]() ![]() References: UniProt: P0A8T7, ![]() #4: Protein/peptide | | ![]() Mass: 10249.547 Da / Num. of mol.: 1 Source: (gene. exp.) ![]() ![]() ![]() Gene: rpoZ, b3649, JW3624 Production host: ![]() ![]() ![]() References: UniProt: P0A800, ![]() |
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-Protein/peptide , 1 types, 1 molecules M
#5: Protein/peptide | Mass: 54723.082 Da / Num. of mol.: 1 / Mutation: R356A,R356A,R356A,R356A,R356A / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: A0A0J4U551, UniProt: P06223*PLUS, ![]() |
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-NifH promoter ... , 2 types, 2 molecules FG
#6: DNA chain | Mass: 19404.410 Da / Num. of mol.: 1 / Source: (synth.) ![]() ![]() |
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#7: DNA chain | Mass: 19487.436 Da / Num. of mol.: 1 / Source: (synth.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / Reconstruction method: ![]() |
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Sample preparation
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Molecular weight | Value: 0.490 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Microscope model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 45 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: REFMAC / Version: 5.8.0158 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 79678 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Ref protocol: RIGID BODY FIT / Ref space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine | Correlation coeff Fo to Fc: 0.918 / Overall SU B: 10.109 / Overall SU ML: 0.155 / Overall ESU R: 0.16 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model details: PARAMETERS FOR MASK CACLULATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | B iso mean: 250.91 / Aniso B11: 2.22 / Aniso B12: -2.37 / Aniso B13: 1.02 / Aniso B22: -1.4 / Aniso B23: -0.32 / Aniso B33: -0.82 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Least-squares process | R factor R work![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Number of atoms included #1 | Total: 28366 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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