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Yorodumi- EMDB-12884: A cooperative PNPase-Hfq-RNA carrier complex facilitates bacteria... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12884 | |||||||||
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Title | A cooperative PNPase-Hfq-RNA carrier complex facilitates bacterial riboregulation. PNPase-3'ETS(leuZ)-Hfq | |||||||||
Map data | Locally filtered cryo-EM map | |||||||||
Sample |
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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 / regulation of DNA-templated transcription ...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 / regulation of DNA-templated transcription / magnesium ion binding / RNA binding / membrane / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Dendooven T / Sinha D / Roesoleva A / Cameron TA / De Lay N / Luisi BF / Bandyra K | |||||||||
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_12884.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-12884-v30.xml emd-12884.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12884_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_12884.png | 87.8 KB | ||
Masks | emd_12884_msk_1.map | 103 MB | Mask map | |
Others | emd_12884_half_map_1.map.gz emd_12884_half_map_2.map.gz | 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12884 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12884 | HTTPS FTP |
-Related structure data
Related structure data | 7ogmMC 7ogkC 7oglC 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_12884.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Locally filtered cryo-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_12884_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_12884_half_map_1.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_12884_half_map_2.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PNPase-3'ETS(LeuZ)-Hfq complex
Entire | Name: PNPase-3'ETS(LeuZ)-Hfq complex |
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Components |
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-Supramolecule #1: PNPase-3'ETS(LeuZ)-Hfq complex
Supramolecule | Name: PNPase-3'ETS(LeuZ)-Hfq complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 318 KDa |
-Macromolecule #1: RNA-binding protein Hfq
Macromolecule | Name: RNA-binding protein Hfq / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 11.179354 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAKGQSLQDP FLNALRRERV PVSIYLVNGI KLQGQIESFD QFVILLKNTV SQMVYKHAIS TVVPSRPVSH HSNNAGGGTS SNYHHGSSA QNTSAQQDSE ETE |
-Macromolecule #2: Polyribonucleotide nucleotidyltransferase
Macromolecule | Name: Polyribonucleotide nucleotidyltransferase / type: protein_or_peptide / ID: 2 / 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 |
-Macromolecule #3: 3'ETS(LeuZ)
Macromolecule | Name: 3'ETS(LeuZ) / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 15.748497 KDa |
Sequence | String: AGAUAAGAAU AAAAUCAAUU UAAAAAAAAA AAAAAAAAAA UUUUUUUUU |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -0.0026000000000000003 µm / Nominal defocus min: -0.001 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-38 / Number grids imaged: 4 / Number real images: 19566 / Average exposure time: 12.0 sec. / Average electron dose: 53.6 e/Å2 |
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-7ogm: |