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Yorodumi- EMDB-15785: CryoEM structure of bacterial RNaseE.RapZ.GlmZ complex central to... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15785 | |||||||||
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Title | CryoEM structure of bacterial RNaseE.RapZ.GlmZ complex central to the control of cell envelope biogenesis | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information regulation of RNA helicase activity / rRNA 5'-end processing / ribonuclease E / ribonuclease E activity / bacterial degradosome / RNA destabilization / endoribonuclease complex / DEAD/H-box RNA helicase binding / carbohydrate derivative binding / 7S RNA binding ...regulation of RNA helicase activity / rRNA 5'-end processing / ribonuclease E / ribonuclease E activity / bacterial degradosome / RNA destabilization / endoribonuclease complex / DEAD/H-box RNA helicase binding / carbohydrate derivative binding / 7S RNA binding / RNA catabolic process / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / protein complex oligomerization / protein homotetramerization / tRNA binding / molecular adaptor activity / rRNA binding / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / zinc ion binding / ATP binding / identical protein binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.99 Å | |||||||||
Authors | Islam MS / Hardwick HW / Chirgadze DY / Luisi BF | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: EMBO J / Year: 2023 Title: Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis. Authors: Md Saiful Islam / Steven W Hardwick / Laura Quell / Svetlana Durica-Mitic / Dimitri Y Chirgadze / Boris Görke / Ben F Luisi / Abstract: Biogenesis of the essential precursor of the bacterial cell envelope, glucosamine-6-phosphate (GlcN6P), is controlled by intricate post-transcriptional networks mediated by GlmZ, a small regulatory ...Biogenesis of the essential precursor of the bacterial cell envelope, glucosamine-6-phosphate (GlcN6P), is controlled by intricate post-transcriptional networks mediated by GlmZ, a small regulatory RNA (sRNA). GlmZ stimulates translation of the mRNA encoding GlcN6P synthtase in Escherichia coli, but when bound by RapZ protein, the sRNA becomes inactivated through cleavage by the endoribonuclease RNase E. Here, we report the cryoEM structure of the RapZ:GlmZ complex, revealing a complementary match of the RapZ tetrameric quaternary structure to structural repeats in the sRNA. The nucleic acid is contacted by RapZ mostly through a highly conserved domain that shares an evolutionary relationship with phosphofructokinase and suggests links between metabolism and riboregulation. We also present the structure of a precleavage intermediate formed between the binary RapZ:GlmZ complex and RNase E that reveals how GlmZ is presented and recognised by the enzyme. The structures provide a framework for understanding how other encounter complexes might guide recognition and action of endoribonucleases on target transcripts, and how structured substrates in polycistronic precursors may be recognised for processing by RNase E. #1: Journal: Biorxiv / Year: 2022 Title: Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis Authors: Islam MS / Hardwick SW / Quell L / Chirgadze DY / Gorke B / Luisi BF | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15785.map.gz | 344.4 MB | EMDB map data format | |
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Header (meta data) | emd-15785-v30.xml emd-15785.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_15785.png | 55.9 KB | ||
Others | emd_15785_half_map_1.map.gz emd_15785_half_map_2.map.gz | 345 MB 345 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15785 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15785 | HTTPS FTP |
-Validation report
Summary document | emd_15785_validation.pdf.gz | 973.7 KB | Display | EMDB validaton report |
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Full document | emd_15785_full_validation.pdf.gz | 973.3 KB | Display | |
Data in XML | emd_15785_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | emd_15785_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15785 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15785 | HTTPS FTP |
-Related structure data
Related structure data | 8b0jMC 8b0iC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15785.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.652 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_15785_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15785_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RapZ tetramer, GlmZ stem loops I & II
Entire | Name: RapZ tetramer, GlmZ stem loops I & II |
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Components |
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-Supramolecule #1: RapZ tetramer, GlmZ stem loops I & II
Supramolecule | Name: RapZ tetramer, GlmZ stem loops I & II / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all / Details: In vitro reconstituted RapZ and GlmZ complex |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: RNase adapter protein RapZ
Macromolecule | Name: RNase adapter protein RapZ / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 32.53832 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MVLMIVSGRS GSGKSVALRA LEDMGFYCVD NLPVVLLPDL ARTLADREIS AAVSIDVRNM PESPEIFEQA MSNLPDAFSP QLLFLDADR NTLIRRYSDT RRLHPLSSKN LSLESAIDKE SDLLEPLRSR ADLIVDTSEM SVHELAEMLR TRLLGKRERE L TMVFESFG ...String: MVLMIVSGRS GSGKSVALRA LEDMGFYCVD NLPVVLLPDL ARTLADREIS AAVSIDVRNM PESPEIFEQA MSNLPDAFSP QLLFLDADR NTLIRRYSDT RRLHPLSSKN LSLESAIDKE SDLLEPLRSR ADLIVDTSEM SVHELAEMLR TRLLGKRERE L TMVFESFG FKHGIPIDAD YVFDVRFLPN PHWDPKLRPM TGLDKPVAAF LDRHTEVHNF IYQTRSYLEL WLPMLETNNR SY LTVAIGC TGGKHRSVYI AEQLADYFRS RGKNVQSRHR TLEKRKP |
-Macromolecule #2: Ribonuclease E
Macromolecule | Name: Ribonuclease E / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease E |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 64.518363 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MKRMLINATQ QEELRVALVD GQRLYDLDIE SPGHEQKKAN IYKGKITRIE PSLEAAFVDY GAERHGFLPL KEIAREYFPA NYSAHGRPN IKDVLREGQE VIVQIDKEER GNKGAALTTF ISLAGSYLVL MPNNPRAGGI SRRIEGDDRT ELKEALASLE L PEGMGLIV ...String: MKRMLINATQ QEELRVALVD GQRLYDLDIE SPGHEQKKAN IYKGKITRIE PSLEAAFVDY GAERHGFLPL KEIAREYFPA NYSAHGRPN IKDVLREGQE VIVQIDKEER GNKGAALTTF ISLAGSYLVL MPNNPRAGGI SRRIEGDDRT ELKEALASLE L PEGMGLIV RTAGVGKSAE ALQWDLSFRL KHWEAIKKAA ESRPAPFLIH QESNVIVRAF RDYLRQDIGE ILIDNPKVLE LA RQHIAAL GRPDFSSKIK LYTGEIPLFS HYQIESQIES AFQREVRLPS GGSIVIDSTE ALTAIDINSA RATRGGDIEE TAF NTNLEA ADEIARQLRL RDLGGLIVIC FIDMTPVRHQ RAVENRLREA VRQDRARIQI SHISRFGLLE MSRQRLSPSL GESS HHVCP RCSGTGTVRD NESLSLSILR LIEEEALKEN TQEVHAIVPV PIASYLLNEK RSAVNAIETR QDGVRCVIVP NDQME TPHY HVLRVRKGEE TPTLSYMLPK LHEEAMALPS EEEFAERKRP EQPALATFAM PDVPPAPTPA EPAAPVVAPA PKAAPA TPA APAGGEETKP TEQPAPKA |
-Macromolecule #3: GlmZ small RNA
Macromolecule | Name: GlmZ small RNA / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 66.061859 KDa |
Sequence | String: GUAGAUGCUC AUUCCAUCUC UUAUGUUCGC CUUAGUGCCU CAUAAACUCC GGAAUGACGC AGAGCCGUUU ACGGUGCUUA UCGUCCACU GACAGAUGUC GCUUAUGCCU CAUCAGACAC CAUGGACACA ACGUUGAGUG AAGCACCCAC UUGUUGUCAU A CAGACCUG ...String: GUAGAUGCUC AUUCCAUCUC UUAUGUUCGC CUUAGUGCCU CAUAAACUCC GGAAUGACGC AGAGCCGUUU ACGGUGCUUA UCGUCCACU GACAGAUGUC GCUUAUGCCU CAUCAGACAC CAUGGACACA ACGUUGAGUG AAGCACCCAC UUGUUGUCAU A CAGACCUG UUUUAACGCC UGCUCCGUUA AUAAGAGCAG GCGUUUUUU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 3D array |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 / Details: 25 mM HEPES pH 7.5, 300 KCl, and 1 mM MgCl2 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 0.3 µm / Nominal defocus min: 0.1 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-8b0j: |