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Yorodumi- EMDB-0592: Architectural principles for Hfq/Crc-mediated regulation of gene ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0592 | |||||||||
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Title | Architectural principles for Hfq/Crc-mediated regulation of gene expression Hfq-Crc-amiE 2:4:2 complex | |||||||||
Map data | Locally sharpened Cryo-EM map of a Hfq-Crc-amiE assembly with stoichiometry 2:4:2, respectively. | |||||||||
Sample |
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Keywords | Hfq / Crc / amiE / Carbon catabolite repression / RNA-protein interaction / RNA-mediated gene regulation / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-HYDROLASE complex | |||||||||
Function / homology | Function and homology information regulation of carbon utilization / regulation of translation, ncRNA-mediated / regulation of RNA stability / quorum sensing / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / regulation of translation / DNA repair / regulation of DNA-templated transcription / RNA binding ...regulation of carbon utilization / regulation of translation, ncRNA-mediated / regulation of RNA stability / quorum sensing / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / regulation of translation / DNA repair / regulation of DNA-templated transcription / RNA binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
Authors | Pei XY / Dendooven T | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Elife / Year: 2019 Title: Architectural principles for Hfq/Crc-mediated regulation of gene expression. Authors: Xue Yuan Pei / Tom Dendooven / Elisabeth Sonnleitner / Shaoxia Chen / Udo Bläsi / Ben F Luisi / Abstract: In diverse bacterial species, the global regulator Hfq contributes to post-transcriptional networks that control expression of numerous genes. Hfq of the opportunistic pathogen inhibits translation ...In diverse bacterial species, the global regulator Hfq contributes to post-transcriptional networks that control expression of numerous genes. Hfq of the opportunistic pathogen inhibits translation of target transcripts by forming a regulatory complex with the catabolite repression protein Crc. This repressive complex acts as part of an intricate mechanism of preferred nutrient utilisation. We describe high-resolution cryo-EM structures of the assembly of Hfq and Crc bound to the translation initiation site of a target mRNA. The core of the assembly is formed through interactions of two cognate RNAs, two Hfq hexamers and a Crc pair. Additional Crc protomers are recruited to the core to generate higher-order assemblies with demonstrated regulatory activity in vivo. This study reveals how Hfq cooperates with a partner protein to regulate translation, and provides a structural basis for an RNA code that guides global regulators to interact cooperatively and regulate different RNA targets. | |||||||||
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_0592.map.gz | 11.7 MB | EMDB map data format | |
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Header (meta data) | emd-0592-v30.xml emd-0592.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0592_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_0592.png | 144.8 KB | ||
Masks | emd_0592_msk_1.map | 26.2 MB | Mask map | |
Filedesc metadata | emd-0592.cif.gz | 7.1 KB | ||
Others | emd_0592_additional.map.gz emd_0592_half_map_1.map.gz emd_0592_half_map_2.map.gz | 24.3 MB 23.3 MB 23.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0592 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0592 | HTTPS FTP |
-Validation report
Summary document | emd_0592_validation.pdf.gz | 876 KB | Display | EMDB validaton report |
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Full document | emd_0592_full_validation.pdf.gz | 875.6 KB | Display | |
Data in XML | emd_0592_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | emd_0592_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0592 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0592 | HTTPS FTP |
-Related structure data
Related structure data | 6o1mMC 0590C 0591C 6o1kC 6o1lC 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_0592.map.gz / Format: CCP4 / Size: 26.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Locally sharpened Cryo-EM map of a Hfq-Crc-amiE assembly with stoichiometry 2:4:2, respectively. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 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_0592_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Globally sharpened Cryo-EM map of a Hfq-Crc-amiE assembly...
File | emd_0592_additional.map | ||||||||||||
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Annotation | Globally sharpened Cryo-EM map of a Hfq-Crc-amiE assembly with stoichiometry 2:4:2, respectively. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_0592_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_0592_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Assembly of Hfq-Crc-amiE with a 2:4:2 stoichiometry
Entire | Name: Assembly of Hfq-Crc-amiE with a 2:4:2 stoichiometry |
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Components |
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-Supramolecule #1: Assembly of Hfq-Crc-amiE with a 2:4:2 stoichiometry
Supramolecule | Name: Assembly of Hfq-Crc-amiE with a 2:4:2 stoichiometry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 252 KDa |
-Macromolecule #1: Catabolite repression control protein
Macromolecule | Name: Catabolite repression control protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: exodeoxyribonuclease III |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 30.101869 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPAMRIISVN VNGIQAAAER GLLSWLQAQN ADVICLQDTR ASAFDLDDPS FQLDGYFLYA CDAELPEQGG VALYSRLQPK AVISGLGFE TADRYGRYLQ ADFDKVSIAT LLLPSGQSGD ESLNQKFKFM DDFTHYLSKQ RRKRREYIYC GSLYVAHQKM D VKNWRECQ ...String: GPAMRIISVN VNGIQAAAER GLLSWLQAQN ADVICLQDTR ASAFDLDDPS FQLDGYFLYA CDAELPEQGG VALYSRLQPK AVISGLGFE TADRYGRYLQ ADFDKVSIAT LLLPSGQSGD ESLNQKFKFM DDFTHYLSKQ RRKRREYIYC GSLYVAHQKM D VKNWRECQ QMPGFLAPER AWLDEVFGNL GYADALREVS REGDQFSWWP DSEQAEMLNL GWRFDYQVLT PGLRRFVRNA KL PRQPRFS QHAPLIVDYD WQLSI UniProtKB: Catabolite repression control protein |
-Macromolecule #2: RNA-binding protein Hfq
Macromolecule | Name: RNA-binding protein Hfq / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 |
Molecular weight | Theoretical: 7.685984 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: HSLQDPYLNT LRKERVPVSI YLVNGIKLQG QIESFDQFVI LLKNTVSQMV YKHAISTVVP SRPVRLP UniProtKB: RNA-binding protein Hfq |
-Macromolecule #3: RNA (5'-R(*AP*AP*AP*AP*AP*UP*AP*AP*CP*AP*AP*CP*AP*AP*GP*AP*GP*G)-3')
Macromolecule | Name: RNA (5'-R(*AP*AP*AP*AP*AP*UP*AP*AP*CP*AP*AP*CP*AP*AP*GP*AP*GP*G)-3') type: rna / ID: 3 / Number of copies: 2 |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 5.85766 KDa |
Sequence | String: AAAAAUAACA ACAAGAGG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 Component:
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Grid | Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Details: unspecified | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K | ||||||||||||
Details | Monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 100.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 917 / Average exposure time: 60.0 sec. / Average electron dose: 28.0 e/Å2 Details: Images were collected in movie-counting mode, 75 frames per movie stack, 60s exposure per movie |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 130841 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.00125 µm / Nominal magnification: 125000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation | ||||||
Output model | PDB-6o1m: |