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- EMDB-16265: Hfq-Crc-estA translation repression complex -

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Basic information

Entry
Database: EMDB / ID: EMD-16265
TitleHfq-Crc-estA translation repression complex
Map dataConsensus map
Sample
  • Complex: Complex of the RNA chaperone Hfq with helper protein Crc assembled on a fragment of estA mRNA
    • Complex: RNA-binding protein Hfq and Catabolite repression control protein
      • Protein or peptide: RNA-binding protein Hfq
      • Protein or peptide: Catabolite repression control protein
    • Complex: estA mRNA
      • RNA: estA mRNA
Function / homology
Function and homology information


exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / DNA repair / regulation of DNA-templated transcription / RNA binding / metal ion binding
Similarity search - Function
Exodeoxyribonuclease III-like / RNA-binding protein Hfq / Hfq protein / AP endonuclease 1 / AP endonucleases family 1 profile. / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / : / Sm domain profile. / Endonuclease/exonuclease/phosphatase superfamily / LSM domain superfamily
Similarity search - Domain/homology
RNA-binding protein Hfq / Catabolite repression control protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsDendooven T / Luisi BF
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: 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
DepositionDec 4, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateFeb 8, 2023-
Current statusFeb 8, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16265.png

Downloads & links

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Map

FileDownload / File: emd_16265.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.14269559 - 0.31319302
Average (Standard dev.)0.0021625462 (±0.012938484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Locally refined map

Fileemd_16265_additional_1.map
AnnotationLocally refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_16265_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_16265_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of the RNA chaperone Hfq with helper protein Crc assemble...

EntireName: Complex of the RNA chaperone Hfq with helper protein Crc assembled on a fragment of estA mRNA
Components
  • Complex: Complex of the RNA chaperone Hfq with helper protein Crc assembled on a fragment of estA mRNA
    • Complex: RNA-binding protein Hfq and Catabolite repression control protein
      • Protein or peptide: RNA-binding protein Hfq
      • Protein or peptide: Catabolite repression control protein
    • Complex: estA mRNA
      • RNA: estA mRNA

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Supramolecule #1: Complex of the RNA chaperone Hfq with helper protein Crc assemble...

SupramoleculeName: Complex of the RNA chaperone Hfq with helper protein Crc assembled on a fragment of estA mRNA
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1, #3, #2
Molecular weightTheoretical: 260 KDa

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Supramolecule #2: RNA-binding protein Hfq and Catabolite repression control protein

SupramoleculeName: RNA-binding protein Hfq and Catabolite repression control protein
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Supramolecule #3: estA mRNA

SupramoleculeName: estA mRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: RNA-binding protein Hfq

MacromoleculeName: RNA-binding protein Hfq / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 9.114487 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSKGHSLQDP YLNTLRKERV PVSIYLVNGI KLQGQIESFD QFVILLKNTV SQMVYKHAIS TVVPSRPVRL PSGDQPAEPG NA

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Macromolecule #2: Catabolite repression control protein

MacromoleculeName: Catabolite repression control protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: exodeoxyribonuclease III
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 30.101869 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: estA mRNA

MacromoleculeName: estA mRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 37.997801 KDa
SequenceString:
GCUGAGGAGG CUUUACGACG GGCCCCGAGG CGCAUGCCGA CGACACGGCG GCCCGACAAU AAAAACAAAU CAUGGAGUAA GAGAAUGAU CAGAAUGGCG CUCAAGCCAC UGGUAGCG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46800

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8bvj:
Hfq-Crc-estA translation repression complex

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