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- PDB-6xav: CryoEM Structure of E. coli Rho-dependent Transcription Pre-termi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xav | ||||||
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Title | CryoEM Structure of E. coli Rho-dependent Transcription Pre-termination Complex bound with NusG | ||||||
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Function / homology | ![]() bacterial-type RNA polymerase core enzyme binding / ATP-dependent activity, acting on RNA / transcription elongation-coupled chromatin remodeling / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hao, Z.T. / Kim, H.K. / Walz, T. / Nudler, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Pre-termination Transcription Complex: Structure and Function. Authors: Zhitai Hao / Vitaly Epshtein / Kelly H Kim / Sergey Proshkin / Vladimir Svetlov / Venu Kamarthapu / Binod Bharati / Alexander Mironov / Thomas Walz / Evgeny Nudler / ![]() ![]() Abstract: Rho is a general transcription termination factor playing essential roles in RNA polymerase (RNAP) recycling, gene regulation, and genomic stability in most bacteria. Traditional models of ...Rho is a general transcription termination factor playing essential roles in RNA polymerase (RNAP) recycling, gene regulation, and genomic stability in most bacteria. Traditional models of transcription termination postulate that hexameric Rho loads onto RNA prior to contacting RNAP and then translocates along the transcript in pursuit of the moving RNAP to pull RNA from it. Here, we report the cryoelectron microscopy (cryo-EM) structures of two termination process intermediates. Prior to interacting with RNA, Rho forms a specific "pre-termination complex" (PTC) with RNAP and elongation factors NusA and NusG, which stabilize the PTC. RNA exiting RNAP interacts with NusA before entering the central channel of Rho from the distal C-terminal side of the ring. We map the principal interactions in the PTC and demonstrate their critical role in termination. Our results support a mechanism in which the formation of a persistent PTC is a prerequisite for termination. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 837 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 22115MC ![]() 6xasC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Transcription termination/antitermination protein ... , 2 types, 2 molecules LG
#1: Protein | Mass: 20560.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#9: Protein | Mass: 54932.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules NT
#2: DNA chain | Mass: 9434.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Non template strand DNA / Source: (synth.) ![]() ![]() ![]() |
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#3: DNA chain | Mass: 8813.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template strand DNA / Source: (synth.) ![]() ![]() ![]() |
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules WKHIJ
#5: Protein | ![]() Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#6: Protein | ![]() Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #7: Protein | | ![]() Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 Production host: ![]() ![]() ![]() ![]() #8: Protein | | ![]() Mass: 156504.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
-RNA chain / Protein , 2 types, 7 molecules RCABDEF
#10: Protein | Mass: 47070.168 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P0AG30, ![]() #4: RNA chain | | Mass: 5859.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
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-Non-polymers , 2 types, 3 molecules ![](data/chem/img/MG.gif)
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#11: Chemical | ChemComp-MG / |
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#12: Chemical |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: E. coli Rho-dependent Transcription Pre-termination Complex Type: COMPLEX / Entity ID: #1-#10 / Source: RECOMBINANT |
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Molecular weight | Value: 0.726 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Specimen support | Details: unspecified |
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57227 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refine LS restraints |
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