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- EMDB-18132: Bacterial transcription termination factor Rho G150D mutant bound... -

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Basic information

Entry
Database: EMDB / ID: EMD-18132
TitleBacterial transcription termination factor Rho G150D mutant bound to ADP; C-terminal 8xHis-tag
Map data
Sample
  • Complex: Filament of Rho mutant G150D
    • Protein or peptide: Transcription termination factor Rho
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsRho / termination / TRANSCRIPTION
Function / homology
Function and homology information


ATP-dependent activity, acting on RNA / DNA-templated transcription termination / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain / Rho termination factor, N-terminal domain superfamily / Cold shock domain ...Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain / Rho termination factor, N-terminal domain superfamily / Cold shock domain / Cold shock protein domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transcription termination factor Rho
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSaid N / Hilal T / Wahl MC
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)433623608 Germany
CitationJournal: bioRxiv / Year: 2023
Title: Transcription termination factor ρ polymerizes under stress.
Authors: Bing Wang / Nelly Said / Tarek Hilal / Mark Finazzo / Markus C Wahl / Irina Artsimovitch /
Abstract: Bacterial RNA helicase ρ is a genome sentinel that terminates synthesis of damaged and junk RNAs that are not translated by the ribosome. Co-transcriptional RNA surveillance by ρ is essential for ...Bacterial RNA helicase ρ is a genome sentinel that terminates synthesis of damaged and junk RNAs that are not translated by the ribosome. Co-transcriptional RNA surveillance by ρ is essential for quality control of the transcriptome during optimal growth. However, it is unclear how bacteria protect their RNAs from overzealous ρ during dormancy or stress, conditions common in natural habitats. Here we used cryogenic electron microscopy, biochemical, and genetic approaches to show that residue substitutions, ADP, or ppGpp promote hyper-oligomerization of ρ. Our results demonstrate that nucleotides bound at subunit interfaces control ρ switching from active hexamers to inactive higher-order oligomers and extended filaments. Polymers formed upon exposure to antibiotics or ppGpp disassemble when stress is relieved, thereby directly linking termination activity to cellular physiology. Inactivation of ρ through hyper-oligomerization is a regulatory strategy shared by RNA polymerases, ribosomes, and metabolic enzymes across all life.
History
DepositionAug 4, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18132.png

Downloads & links

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Map

FileDownload / File: emd_18132.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.0 - 1.4611247
Average (Standard dev.)0.014750103 (±0.06636354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18132_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18132_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Filament of Rho mutant G150D

EntireName: Filament of Rho mutant G150D
Components
  • Complex: Filament of Rho mutant G150D
    • Protein or peptide: Transcription termination factor Rho
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Filament of Rho mutant G150D

SupramoleculeName: Filament of Rho mutant G150D / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Transcription termination factor Rho

MacromoleculeName: Transcription termination factor Rho / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Escherichia (bacteria)
Molecular weightTheoretical: 48.616809 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHMNLTELK NTPVSELITL GENMGLENLA RMRKQDIIFA ILKQHAKSGE DIFGDGVLEI LQDGFGFLRS ADSSYLAGPD DIYVSPSQI RRFNLRTGDT ISGKIRPPKE GERYFALLKV NEVNFDKPEN ARNKILFENL TPLHANSRLR MERDNGSTED L TARVLDLA ...String:
MGHMNLTELK NTPVSELITL GENMGLENLA RMRKQDIIFA ILKQHAKSGE DIFGDGVLEI LQDGFGFLRS ADSSYLAGPD DIYVSPSQI RRFNLRTGDT ISGKIRPPKE GERYFALLKV NEVNFDKPEN ARNKILFENL TPLHANSRLR MERDNGSTED L TARVLDLA SPIGRGQRGL IVAPPKAGKT MLLQNIAQSI AYNHPDCVLM VLLIDERPEE VTEMQRLVKG EVVASTFDEP AS RHVQVAE MVIEKAKRLV EHKKDVIILL DSITRLARAY NTVVPASGKV LTGGVDANAL HRPKRFFGAA RNVEEGGSLT IIA TALIDT GSKMDEVIYE EFKGTGNMEL HLSRKIAEKR VFPAIDYNRS GTRKEELLTT QEELQKMWIL RKIIHPMGEI DAME FLINK LAMTKTNDDF FEMMKRSGHH HHHHHH

UniProtKB: Transcription termination factor Rho

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 18 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 18 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.4 mg/mL
BufferpH: 7.6
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2511 / Average exposure time: 40.57 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 10.76 Å
Applied symmetry - Helical parameters - Δ&Phi: 54.26 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140359
Segment selectionNumber selected: 495704
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 96.4
Output model

PDB-8q3p:
Bacterial transcription termination factor Rho G150D mutant bound to ADP; C-terminal 8xHis-tag

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