+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16647 | |||||||||
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Title | Cryo-EM structure of RNase J from Helicobacter pylori | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ribonuclease / RNase J / degradosome / Helicobacter pylori / RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information 5'-3' RNA exonuclease activity / RNA endonuclease activity / regulation of cell growth / mRNA processing / rRNA processing / protein homotetramerization / Hydrolases; Acting on ester bonds / protein homodimerization activity / RNA binding / zinc ion binding ...5'-3' RNA exonuclease activity / RNA endonuclease activity / regulation of cell growth / mRNA processing / rRNA processing / protein homotetramerization / Hydrolases; Acting on ester bonds / protein homodimerization activity / RNA binding / zinc ion binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Helicobacter pylori (bacteria) / Helicobacter pylori B128 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Lulla A / Luisi BF | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Acetylation regulates the oligomerization state and activity of RNase J, the Helicobacter pylori major ribonuclease. Authors: Alejandro Tejada-Arranz / Aleksei Lulla / Maxime Bouilloux-Lafont / Evelyne Turlin / Xue-Yuan Pei / Thibaut Douché / Mariette Matondo / Allison H Williams / Bertrand Raynal / Ben F Luisi / Hilde De Reuse / Abstract: In the gastric pathogen Helicobacter pylori, post-transcriptional regulation relies strongly on the activity of the essential ribonuclease RNase J. Here, we elucidated the crystal and cryo-EM ...In the gastric pathogen Helicobacter pylori, post-transcriptional regulation relies strongly on the activity of the essential ribonuclease RNase J. Here, we elucidated the crystal and cryo-EM structures of RNase J and determined that it assembles into dimers and tetramers in vitro. We found that RNase J extracted from H. pylori is acetylated on multiple lysine residues. Alanine substitution of several of these residues impacts on H. pylori morphology, and thus on RNase J function in vivo. Mutations of Lysine 649 modulates RNase J oligomerization in vitro, which in turn influences ribonuclease activity in vitro. Our structural analyses of RNase J reveal loops that gate access to the active site and rationalizes how acetylation state of K649 can influence activity. We propose acetylation as a regulatory level controlling the activity of RNase J and its potential cooperation with other enzymes of RNA metabolism in H. pylori. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16647.map.gz | 31.7 MB | EMDB map data format | |
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Header (meta data) | emd-16647-v30.xml emd-16647.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16647_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_16647.png | 61.3 KB | ||
Masks | emd_16647_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-16647.cif.gz | 6 KB | ||
Others | emd_16647_half_map_1.map.gz emd_16647_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16647 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16647 | HTTPS FTP |
-Validation report
Summary document | emd_16647_validation.pdf.gz | 757.6 KB | Display | EMDB validaton report |
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Full document | emd_16647_full_validation.pdf.gz | 757.2 KB | Display | |
Data in XML | emd_16647_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_16647_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16647 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16647 | HTTPS FTP |
-Related structure data
Related structure data | 8cglMC 7pcrC 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_16647.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.106 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16647_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16647_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16647_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Helicobacter pylori RNase J
Entire | Name: Helicobacter pylori RNase J |
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Components |
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-Supramolecule #1: Helicobacter pylori RNase J
Supramolecule | Name: Helicobacter pylori RNase J / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Helicobacter pylori (bacteria) / Strain: B128 |
Molecular weight | Theoretical: 316 KDa |
-Macromolecule #1: Ribonuclease J
Macromolecule | Name: Ribonuclease J / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: Helicobacter pylori B128 (bacteria) |
Molecular weight | Theoretical: 79.19693 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GSGTDNNHYE NNESNENSSE NSKVDEARAG AFERFTNRKK RFRENAQKNG ESSHHEAPSH HKKEHRPNKK PNNHHKQKHA KTRNYAKEE LDSNKVEGVT EILHVNERGT LGFHKELKKG VETNNKIQVE HLNPHYKMNL NSKASVKITP LGGLGEIGGN M MVIETPKS ...String: GSGTDNNHYE NNESNENSSE NSKVDEARAG AFERFTNRKK RFRENAQKNG ESSHHEAPSH HKKEHRPNKK PNNHHKQKHA KTRNYAKEE LDSNKVEGVT EILHVNERGT LGFHKELKKG VETNNKIQVE HLNPHYKMNL NSKASVKITP LGGLGEIGGN M MVIETPKS AIVIDAGMSF PKEGLFGVDI LIPDFSYLHQ IKDKIAGIII THAHEDHIGA TPYLFKELQF PLYGTPLSLG LI GSKFDEH GLKKYRSYFK IVEKRCPISV GEFIIEWIHI THSIIDSSAL AIQTKAGTII HTGDFKIDHT PVDNLPTDLY RLA HYGEKG VMLLLSDSTN SHKSGTTPSE STIAPAFDTL FKEAQGRVIM STFSSNIHRV YQAIQYGIKY NRKIAVIGRS MEKN LDIAR ELGYIHLPYQ SFIEANEVAK YPDNEVLIVT TGSQGETMSA LYRMATDEHR HISIKPNDLV IISAKAIPGN EASVS AVLN FLIKKEAKVA YQEFDNIHVS GHAAQEEQKL MLRLIKPKFF LPVHGEYNHV ARHKQTAISC GVPEKNIYLM EDGDQV EVG PAFIKKVGTI KSGKSYVDNQ SNLSIDTSIV QQREEVASAG VFAATIFVNK NKQALLESSQ FSSLGLVGFK DEKPLIK EI QGGLEMLLKS SNAEILNNPK KLEDHTRNFI RKALFKKFRK YPAIICHAHS FGSSPHHHHH HHH UniProtKB: Ribonuclease J |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.029 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.58 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |