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Yorodumi- EMDB-12882: A cooperative PNPase-Hfq-RNA carrier complex facilitates bacteria... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12882 | |||||||||
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Title | A cooperative PNPase-Hfq-RNA carrier complex facilitates bacterial riboregulation. PNPase-3'ETS(leuZ) | |||||||||
Map data | Locally filtered EM map | |||||||||
Sample |
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Keywords | RNA chaperone / Ribonuclease / Small regulatory RNA / Riboregulation / RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Dendooven T / Sinha D | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Mol Cell / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12882.map.gz | 3.8 MB | EMDB map data format | |
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Header (meta data) | emd-12882-v30.xml emd-12882.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12882_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_12882.png | 82.9 KB | ||
Masks | emd_12882_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-12882.cif.gz | 6.1 KB | ||
Others | emd_12882_half_map_1.map.gz emd_12882_half_map_2.map.gz | 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12882 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12882 | HTTPS FTP |
-Validation report
Summary document | emd_12882_validation.pdf.gz | 909.7 KB | Display | EMDB validaton report |
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Full document | emd_12882_full_validation.pdf.gz | 909.3 KB | Display | |
Data in XML | emd_12882_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | emd_12882_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12882 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12882 | HTTPS FTP |
-Related structure data
Related structure data | 7ogkMC 7oglC 7ogmC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12882.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Locally filtered EM map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12882_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_12882_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12882_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PNPase
Entire | Name: PNPase |
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Components |
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-Supramolecule #1: PNPase
Supramolecule | Name: PNPase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 253 KDa |
-Macromolecule #1: Polyribonucleotide nucleotidyltransferase
Macromolecule | Name: Polyribonucleotide nucleotidyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: polyribonucleotide nucleotidyltransferase |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 77.189844 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLNPIVRKFQ YGQHTVTLET GMMARQATAA VMVSMDDTAV FVTVVGQKKA KPGQDFFPLT VNYQERTYAA GRIPGSFFRR EGRPSEGET LIARLIDRPI RPLFPEGFVN EVQVIATVVS VNPQVNPDIV AMIGASAALS LSGIPFNGPI GAARVGYIND Q YVLNPTQD ...String: MLNPIVRKFQ YGQHTVTLET GMMARQATAA VMVSMDDTAV FVTVVGQKKA KPGQDFFPLT VNYQERTYAA GRIPGSFFRR EGRPSEGET LIARLIDRPI RPLFPEGFVN EVQVIATVVS VNPQVNPDIV AMIGASAALS LSGIPFNGPI GAARVGYIND Q YVLNPTQD ELKESKLDLV VAGTEAAVLM VESEAQLLSE DQMLGAVVFG HEQQQVVIQN INELVKEAGK PRWDWQPEPV NE ALNARVA ALAEARLSDA YRITDKQERY AQVDVIKSET IATLLAEDET LDENELGEIL HAIEKNVVRS RVLAGEPRID GRE KDMIRG LDVRTGVLPR THGSALFTRG ETQALVTATL GTARDAQVLD ELMGERTDTF LFHYNFPPYS VGETGMVGSP KRRE IGHGR LAKRGVLAVM PDMDKFPYTV RVVSEITESN GSSSMASVCG ASLALMDAGV PIKAAVAGIA MGLVKEGDNY VVLSD ILGD EDHLGDMDFK VAGSRDGISA LQMDIKIEGI TKEIMQVALN QAKGARLHIL GVMEQAINAP RGDISEFAPR IHTIKI NPD KIKDVIGKGG SVIRALTEET GTTIEIEDDG TVKIAATDGE KAKHAIRRIE EITAEIEVGR VYTGKVTRIV DFGAFVA IG GGKEGLVHIS QIADKRVEKV TDYLQMGQEV PVKVLEVDRQ GRIRLSIKEA TEQSQPAAAP EAPAAEQGE UniProtKB: Polyribonucleotide nucleotidyltransferase |
-Macromolecule #2: 3'ETS(LeuZ)
Macromolecule | Name: 3'ETS(LeuZ) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 2.588689 KDa |
Sequence | String: AAAAAAAA |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 17 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-38 / Number grids imaged: 1 / Number real images: 2741 / Average exposure time: 12.0 sec. / Average electron dose: 53.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -0.0026000000000000003 µm / Nominal defocus min: -0.001 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-7ogk: |