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Yorodumi- EMDB-16266: Cryo-EM structure of Hfq-Crc-rbsB translation repression complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16266 | |||||||||
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Title | Cryo-EM structure of Hfq-Crc-rbsB translation repression complex | |||||||||
Map data | Locally filtered map | |||||||||
Sample |
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Keywords | co-transcriptional RNA folding / Crc / metabolic regulation / ribonucleoprotein assembly / RNA chaperone Hfq / translational regulation / RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information regulation of translation, ncRNA-mediated / regulation of RNA stability / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA repair / regulation of DNA-templated transcription / RNA binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Dendooven T / Luisi BF | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: EMBO J / Year: 2023 Title: Translational regulation by Hfq-Crc assemblies emerges from polymorphic ribonucleoprotein folding. Authors: Tom Dendooven / Elisabeth Sonnleitner / Udo Bläsi / Ben F Luisi / Abstract: The widely occurring bacterial RNA chaperone Hfq is a key factor in the post-transcriptional control of hundreds of genes in Pseudomonas aeruginosa. How this broadly acting protein can contribute to ...The widely occurring bacterial RNA chaperone Hfq is a key factor in the post-transcriptional control of hundreds of genes in Pseudomonas aeruginosa. How this broadly acting protein can contribute to the regulatory requirements of many different genes remains puzzling. Here, we describe cryo-EM structures of higher order assemblies formed by Hfq and its partner protein Crc on control regions of different P. aeruginosa target mRNAs. Our results show that these assemblies have mRNA-specific quaternary architectures resulting from the combination of multivalent protein-protein interfaces and recognition of patterns in the RNA sequence. The structural polymorphism of these ribonucleoprotein assemblies enables selective translational repression of many different target mRNAs. This system elucidates how highly complex regulatory pathways can evolve with a minimal economy of proteinogenic components in combination with RNA sequence and fold. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16266.map.gz | 7.3 MB | EMDB map data format | |
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Header (meta data) | emd-16266-v30.xml emd-16266.xml | 21.1 KB 21.1 KB | Display Display | EMDB header |
Images | emd_16266.png | 77.3 KB | ||
Filedesc metadata | emd-16266.cif.gz | 7.7 KB | ||
Others | emd_16266_additional_1.map.gz emd_16266_half_map_1.map.gz emd_16266_half_map_2.map.gz | 63.9 MB 95.6 MB 95.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16266 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16266 | HTTPS FTP |
-Related structure data
Related structure data | 8bvmMC 8bvhC 8bvjC C: citing same article (ref.) M: atomic model generated by this map |
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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_16266.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Locally filtered map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Denoised map
File | emd_16266_additional_1.map | ||||||||||||
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Annotation | Denoised map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_16266_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_16266_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of the RNA chaperone Hfq and helper protein Crc assembled...
Entire | Name: Complex of the RNA chaperone Hfq and helper protein Crc assembled on a rbsB mRNA fragment |
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Components |
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-Supramolecule #1: Complex of the RNA chaperone Hfq and helper protein Crc assembled...
Supramolecule | Name: Complex of the RNA chaperone Hfq and helper protein Crc assembled on a rbsB mRNA fragment type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 180 KDa |
-Supramolecule #2: Catabolite repression control protein
Supramolecule | Name: Catabolite repression control protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
-Supramolecule #3: rbsB mRNA
Supramolecule | Name: rbsB mRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
-Supramolecule #4: RNA-binding protein Hfq
Supramolecule | Name: RNA-binding protein Hfq / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
-Macromolecule #1: Catabolite repression control protein
Macromolecule | Name: Catabolite repression control protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / 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: Pseudomonas aeruginosa (bacteria) |
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 (bacteria) |
Molecular weight | Theoretical: 9.114487 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSKGHSLQDP YLNTLRKERV PVSIYLVNGI KLQGQIESFD QFVILLKNTV SQMVYKHAIS TVVPSRPVRL PSGDQPAEPG NA UniProtKB: RNA-binding protein Hfq |
-Macromolecule #3: rbsB mRNA
Macromolecule | Name: rbsB mRNA / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 34.850766 KDa |
Sequence | String: AACGCAAACG UUUGCGUCUG GAUAAUCUCC UGGAAAAGAA UCAAUACAAC GAUAAGAAAA GCUGGAGGAU AUACCAUGAA GCGGGUCGC UUCCCGGCGC CUGUUGGCU |
-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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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 148700 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15) |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8bvm: |