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- PDB-7ogk: A cooperative PNPase-Hfq-RNA carrier complex facilitates bacteria... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ogk | ||||||
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Title | A cooperative PNPase-Hfq-RNA carrier complex facilitates bacterial riboregulation. PNPase-3'ETS(leuZ) | ||||||
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![]() | RNA BINDING PROTEIN / RNA chaperone / Ribonuclease / Small regulatory RNA / Riboregulation | ||||||
Function / homology | ![]() polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / bacterial degradosome / cyclic-di-GMP binding / RNA catabolic process / mRNA catabolic process / RNA processing / 3'-5'-RNA exonuclease activity / response to heat / magnesium ion binding ...polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / bacterial degradosome / cyclic-di-GMP binding / RNA catabolic process / mRNA catabolic process / RNA processing / 3'-5'-RNA exonuclease activity / response to heat / magnesium ion binding / RNA binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
![]() | Dendooven, T. / Sinha, D. / Roesoleva, A. / Cameron, T.A. / De Lay, N. / Luisi, B.F. / Bandyra, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A cooperative PNPase-Hfq-RNA carrier complex facilitates bacterial riboregulation. Authors: Tom Dendooven / Dhriti Sinha / Alzbeta Roeselová / Todd A Cameron / Nicholas R De Lay / Ben F Luisi / Katarzyna J Bandyra / ![]() ![]() Abstract: Polynucleotide phosphorylase (PNPase) is an ancient exoribonuclease conserved in the course of evolution and is found in species as diverse as bacteria and humans. Paradoxically, Escherichia coli ...Polynucleotide phosphorylase (PNPase) is an ancient exoribonuclease conserved in the course of evolution and is found in species as diverse as bacteria and humans. Paradoxically, Escherichia coli PNPase can act not only as an RNA degrading enzyme but also by an unknown mechanism as a chaperone for small regulatory RNAs (sRNAs), with pleiotropic consequences for gene regulation. We present structures of the ternary assembly formed by PNPase, the RNA chaperone Hfq, and sRNA and show that this complex boosts sRNA stability in vitro. Comparison of structures for PNPase in RNA carrier and degradation modes reveals how the RNA is rerouted away from the active site through interactions with Hfq and the KH and S1 domains. Together, these data explain how PNPase is repurposed to protect sRNAs from cellular ribonucleases such as RNase E and could aid RNA presentation to facilitate regulatory actions on target genes. | ||||||
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 | ![]() | 376.8 KB | Display | ![]() |
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PDB format | ![]() | 299.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 12882MC ![]() 7oglC ![]() 7ogmC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 77189.844 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: pnp, b3164, JW5851 / Production host: ![]() ![]() References: UniProt: P05055, polyribonucleotide nucleotidyltransferase #2: RNA chain | | Mass: 2588.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: PNPase / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.253 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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 / Nominal magnification: 130000 X / Nominal defocus max: -2.6 nm / Nominal defocus min: -1 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 12 sec. / Electron dose: 53.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2741 |
Image scans | Movie frames/image: 38 / Used frames/image: 1-38 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 206803 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |