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- EMDB-17870: Structure of the transcription termination factor Rho bound to RN... -
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Open data
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Basic information
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Title | Structure of the transcription termination factor Rho bound to RNA at the PBS and SBS | |||||||||
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![]() | Transcription termination factor Rho Inhibition of termination Sm-like protein Rof Rho regulation / TRANSCRIPTION RNA binding PBS SBS / TRANSCRIPTION | |||||||||
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 / identical protein binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 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 | ![]() | 83.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.9 KB 17.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.9 KB | Display | ![]() |
Images | ![]() | 25.3 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() | 318.1 MB 318.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ptgMC ![]() 8ptmC ![]() 8ptnC ![]() 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
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Voxel size | X=Y=Z: 0.657 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: EM Half map B
File | emd_17870_half_map_1.map | ||||||||||||
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Annotation | EM Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EM half map A
File | emd_17870_half_map_2.map | ||||||||||||
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Annotation | EM half map A | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Rho-RNA complex
Entire | Name: Rho-RNA complex |
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Components |
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-Supramolecule #1: Rho-RNA complex
Supramolecule | Name: Rho-RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: Rho hexamer in a closed conformation bound to RNA at the PBS and SBS |
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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: rut RNA
Macromolecule | Name: rut RNA / type: rna / ID: 2 / Details: build nucleotides in the structure / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 31.693904 KDa |
Sequence | String: GGGAUAACCC CGCUCUUACA CAUUCCAGCC CUGAAAAAGG GCAUCAAAUU AAACCACACC UAUGGUGUAU GUCAAAUUAA ACCACACCU GGCGUGUGGC |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 5 / 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: 8 |
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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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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3312 / 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 / Nominal magnification: 120000 |
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 / Details: own experimental data |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 94 |
Output model | ![]() PDB-8ptg: |