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- EMDB-17875: Structure of the transcription termination factor Rho in complex ... -
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Open data
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Basic information
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Title | Structure of the transcription termination factor Rho in complex with Rof | |||||||||
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![]() | Transcription termination factor Rho Inhibition of termination Sm-like protein Rof Rho regulation / TRANSCRIPTION | |||||||||
Function / homology | ![]() regulation of termination of DNA-templated transcription / ATP-dependent activity, acting on RNA / helicase activity / transcription antitermination / 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 / identical protein binding ...regulation of termination of DNA-templated transcription / ATP-dependent activity, acting on RNA / helicase activity / transcription antitermination / 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 / identical protein binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Said N / Hilal T / Wahl MC | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation. Authors: Nelly Said / Mark Finazzo / Tarek Hilal / Bing Wang / Tim Luca Selinger / Daniela Gjorgjevikj / Irina Artsimovitch / Markus C Wahl / ![]() ![]() ![]() Abstract: Transcription termination factor ρ is a hexameric, RNA-dependent NTPase that can adopt active closed-ring and inactive open-ring conformations. The Sm-like protein Rof, a homolog of the RNA ...Transcription termination factor ρ is a hexameric, RNA-dependent NTPase that can adopt active closed-ring and inactive open-ring conformations. The Sm-like protein Rof, a homolog of the RNA chaperone Hfq, inhibits ρ-dependent termination in vivo but recapitulation of this activity in vitro has proven difficult and the precise mode of Rof action is presently unknown. Here, our cryo-EM structures of ρ-Rof and ρ-RNA complexes show that Rof undergoes pronounced conformational changes to bind ρ at the protomer interfaces, undercutting ρ conformational dynamics associated with ring closure and occluding extended primary RNA-binding sites that are also part of interfaces between ρ and RNA polymerase. Consistently, Rof impedes ρ ring closure, ρ-RNA interactions and ρ association with transcription elongation complexes. Structure-guided mutagenesis coupled with functional assays confirms that the observed ρ-Rof interface is required for Rof-mediated inhibition of cell growth and ρ-termination in vitro. Bioinformatic analyses reveal that Rof is restricted to Pseudomonadota and that the ρ-Rof interface is conserved. Genomic contexts of rof differ between Enterobacteriaceae and Vibrionaceae, suggesting distinct modes of Rof regulation. We hypothesize that Rof and other cellular anti-terminators silence ρ under diverse, but yet to be identified, stress conditions when unrestrained transcription termination by ρ may be detrimental. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 51.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.3 KB 18.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.7 KB | Display | ![]() |
Images | ![]() | 95.5 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 200.3 MB 200.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ptnMC ![]() 8ptgC ![]() 8ptmC ![]() 8ptoC ![]() 8ptpC M: atomic model generated by this map C: citing same article ( |
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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
File | ![]() | ||||||||||||||||||||
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Annotation | EM map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map B
File | emd_17875_half_map_1.map | ||||||||||||
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Annotation | Half_map_B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_17875_half_map_2.map | ||||||||||||
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Annotation | Half_map_A | ||||||||||||
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Sample components
-Entire : Rho-Rof complex
Entire | Name: Rho-Rof complex |
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Components |
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-Supramolecule #1: Rho-Rof complex
Supramolecule | Name: Rho-Rof complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Rho hexamer in complex with five Rof proteins |
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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 EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 47.070168 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNLTELKNTP VSELITLGEN MGLENLARMR KQDIIFAILK QHAKSGEDIF GDGVLEILQD GFGFLRSADS SYLAGPDDIY VSPSQIRRF NLRTGDTISG KIRPPKEGER YFALLKVNEV NFDKPENARN KILFENLTPL HANSRLRMER GNGSTEDLTA R VLDLASPI ...String: MNLTELKNTP VSELITLGEN MGLENLARMR KQDIIFAILK QHAKSGEDIF GDGVLEILQD GFGFLRSADS SYLAGPDDIY VSPSQIRRF NLRTGDTISG KIRPPKEGER YFALLKVNEV NFDKPENARN KILFENLTPL HANSRLRMER GNGSTEDLTA R VLDLASPI GRGQRGLIVA PPKAGKTMLL QNIAQSIAYN HPDCVLMVLL IDERPEEVTE MQRLVKGEVV ASTFDEPASR HV QVAEMVI EKAKRLVEHK KDVIILLDSI TRLARAYNTV VPASGKVLTG GVDANALHRP KRFFGAARNV EEGGSLTIIA TAL IDTGSK MDEVIYEEFK GTGNMELHLS RKIAEKRVFP AIDYNRSGTR KEELLTTQEE LQKMWILRKI IHPMGEIDAM EFLI NKLAM TKTNDDFFEM MKRS UniProtKB: Transcription termination factor Rho |
-Macromolecule #2: Protein rof
Macromolecule | Name: Protein rof / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 9.618758 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: AMGNDTYQPI NCDDYDNLEL ACQHHLMLTL ELKDGEKLQA KASDLVSRKN VEYLVVEAAG ETRELRLDKI TSFSHPEIGT VVVSES UniProtKB: Protein rof |
-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: 8 |
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Grid | Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Software | Name: EPU (ver. 2.8) |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1555 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Chain ID: A / Chain - Residue range: 1-419 / Chain - Source name: Other / Chain - Initial model type: experimental model / Details: own experimental data |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 98 |
Output model | ![]() PDB-8ptn: |