[English] 日本語
Yorodumi
- EMDB-0590: Architectural principles for Hfq/Crc-mediated regulation of gene ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0590
TitleArchitectural principles for Hfq/Crc-mediated regulation of gene expression Hfq-Crc-amiE 2:2:2 complex (core complex)
Map dataHfq-Crc-amiE 2:2:2 complex
Sample
  • Complex: Assembly of Hfq-Crc-amiE with a 2:2:2 stoichiometry
    • Protein or peptide: Catabolite repression control protein
    • Protein or peptide: RNA-binding protein Hfq
    • RNA: RNA (5'-R(*AP*AP*AP*AP*AP*UP*AP*AP*CP*AP*AP*CP*AP*AP*GP*AP*GP*G)-3')
KeywordsHfq / 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 translation, ncRNA-mediated / regulation of carbon utilization / 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 translation, ncRNA-mediated / regulation of carbon utilization / 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
Exodeoxyribonuclease III-like / RNA-binding protein Hfq / Hfq protein / AP endonuclease 1 / AP endonucleases family 1 profile. / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / : / Sm domain profile. / LSM domain superfamily
Similarity search - Domain/homology
Catabolite repression control protein / RNA-binding protein Hfq
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsPei XY / Dendooven T
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust200873/Z/16/Z United Kingdom
CitationJournal: 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
DepositionFeb 20, 2019-
Header (metadata) releaseMar 13, 2019-
Map releaseMar 13, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6o1k
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0590.png

Downloads & links

-
Map

FileDownload / File: emd_0590.map.gz / Format: CCP4 / Size: 26.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHfq-Crc-amiE 2:2:2 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 190 pix.
= 207.1 Å		1.09 Å/pix.
x 190 pix.
= 207.1 Å		1.09 Å/pix.
x 190 pix.
= 207.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.12181189 - 0.21099027
Average (Standard dev.)-0.000017216207 (±0.009692573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions190190190
Spacing190190190
CellA=B=C: 207.1 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z190190190
origin x/y/z0.0000.0000.000
length x/y/z207.100207.100207.100
α/β/γ90.00090.00090.000
start NX/NY/NZ-205-205-205
NX/NY/NZ411411411
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS190190190
D min/max/mean-0.1220.211-0.000

-
Supplemental data

-
Mask #1

Fileemd_0590_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 Hfq-Crc-amiE 2:2:2 complex

Fileemd_0590_half_map_1.map
AnnotationHalf map 1 Hfq-Crc-amiE 2:2:2 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 Hfq-Crc-amiE 2:2:2 complex

Fileemd_0590_half_map_2.map
AnnotationHalf map 2 Hfq-Crc-amiE 2:2:2 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Assembly of Hfq-Crc-amiE with a 2:2:2 stoichiometry

EntireName: Assembly of Hfq-Crc-amiE with a 2:2:2 stoichiometry
Components
  • Complex: Assembly of Hfq-Crc-amiE with a 2:2:2 stoichiometry
    • Protein or peptide: Catabolite repression control protein
    • Protein or peptide: RNA-binding protein Hfq
    • RNA: RNA (5'-R(*AP*AP*AP*AP*AP*UP*AP*AP*CP*AP*AP*CP*AP*AP*GP*AP*GP*G)-3')

-
Supramolecule #1: Assembly of Hfq-Crc-amiE with a 2:2:2 stoichiometry

SupramoleculeName: Assembly of Hfq-Crc-amiE with a 2:2:2 stoichiometry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 192 KDa

-
Macromolecule #1: Catabolite repression control protein

MacromoleculeName: Catabolite repression control protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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

UniProtKB: Catabolite repression control protein

-
Macromolecule #2: RNA-binding protein Hfq

MacromoleculeName: RNA-binding protein Hfq / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
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 weightTheoretical: 7.685984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
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')

MacromoleculeName: 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
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 5.85766 KDa
SequenceString:
AAAAAUAACA ACAAGAGG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.9
Component:
ConcentrationName
20.0 mMHEPES pH 7.9
40.0 mMNaCl
10.0 mMKCl
1.0 mMMgCl2
2.0 mMTCEP
GridSupport film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K
DetailsMonodisperse

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 100.0 K
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 435000
Startup modelType of model: INSILICO MODEL / In silico model: ab-initio map generated in Relion3
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3b) / Number images used: 73187
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3b) / Software - details: beta version / Details: Stochastic Gradient Descent
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3b) / Software - details: beta version
Final 3D classificationNumber classes: 6 / Avg.num./class: 35000 / Software - Name: RELION (ver. 3b) / Software - details: beta version
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

1u1t

source_name: PDB, initial_model_type: experimental model

4jg3

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation
Output model

PDB-6o1k:
Architectural principles for Hfq/Crc-mediated regulation of gene expression. Hfq-Crc-amiE 2:2:2 complex (core complex)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more