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- EMDB-34999: Thermus thermophilus transcription termination factor Rho bound w... -
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Open data
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Basic information
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Title | Thermus thermophilus transcription termination factor Rho bound with ADP-BeF3 | |||||||||
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Function / homology | ![]() ATP-dependent activity, acting on RNA / helicase activity / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ATP hydrolysis activity / RNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Murayama Y / Ehara H / Sekine S | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from . Authors: Yuko Murayama / Haruhiko Ehara / Mari Aoki / Mie Goto / Takeshi Yokoyama / Shun-Ichi Sekine / ![]() Abstract: Transcription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, transcription termination is mediated by the ...Transcription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, transcription termination is mediated by the adenosine triphosphate-dependent RNA translocase/helicase Rho, which causes RNA/DNA dissociation from the RNAP elongation complex (EC). However, the structural basis of the interplay between Rho and RNAP remains obscure. Here, we report the cryo-electron microscopy structure of the RNAP EC engaged with Rho. The Rho hexamer binds RNAP through the carboxyl-terminal domains, which surround the RNA exit site of RNAP, directing the nascent RNA seamlessly from the RNA exit to its central channel. The β-flap tip at the RNA exit is critical for the Rho-dependent RNA release, and its deletion causes an alternative Rho-RNAP binding mode, which is irrelevant to termination. The Rho binding site overlaps with the binding sites of other macromolecules, such as ribosomes, providing a general basis of gene regulation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 96.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.8 KB 15.8 KB | Display Display | ![]() |
Images | ![]() | 72.4 KB | ||
Others | ![]() ![]() | 97.3 MB 97.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 795.7 KB | Display | ![]() |
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Full document | ![]() | 795.3 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hsjMC ![]() 8hsgC ![]() 8hshC ![]() 8hslC ![]() 8hsrC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34999_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34999_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Transcription termination factor Rho
Entire | Name: Transcription termination factor Rho |
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Components |
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-Supramolecule #1: Transcription termination factor Rho
Supramolecule | Name: Transcription termination factor Rho / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Transcription termination factor Rho
Macromolecule | Name: Transcription termination factor Rho / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 47.99627 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPMRRKETLQ ETPLTYQELA SKILPELHLL AQEAGIEGYK RMKKDQLIMA LLERQTQGEG LRLVKGYLEI SQDGYGFLTE NLHNLESRV AIVSAGLIKQ YALRAGDYVV GQARPPRENE RYATLLKVEA VNNLDPEAAK NRPRFDELTP QFPDRQIRLE T TPDELSTR ...String: GPMRRKETLQ ETPLTYQELA SKILPELHLL AQEAGIEGYK RMKKDQLIMA LLERQTQGEG LRLVKGYLEI SQDGYGFLTE NLHNLESRV AIVSAGLIKQ YALRAGDYVV GQARPPRENE RYATLLKVEA VNNLDPEAAK NRPRFDELTP QFPDRQIRLE T TPDELSTR VIDLLAPIGR GQRGLIVAPP KAGKTTLLKK IANAVLKNEP DIKVIVLLID ERPEEVTDFR ESVQGAEVIA ST FDEPPQN HIRVAEFVHE RAKRIVEEGG HVMILLDSIT RLARANNLVT PPTGRTLSGG LDSAALYFPK RFLGAARNIR GGG SLTILA TALVETGSRM DDVIFEEFKG TGNMELHLSR RLEERRIFPA IDILKSGTRR EELLLGEEVT HKMWLLRKVL ADMD PAEAM EMLLARLART KNNKEFLASL AAR |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ![]() ChemComp-BEF: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 205226 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |