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- PDB-9gcs: Rho-ATP-Psu complex II -

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Basic information

Entry
Database: PDB / ID: 9gcs
TitleRho-ATP-Psu complex II
Components
  • Polarity suppression protein
  • Transcription termination factor Rho
KeywordsTRANSCRIPTION / Transcription termination / Phage inhibitor / GENE REGULATION
Function / homology
Function and homology information


symbiont-mediated activation of host transcription / ATP-dependent activity, acting on RNA / helicase activity / DNA-templated transcription termination / 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
Bacteriophage P4, Psu, polarity suppression protein / Phage polarity suppression protein (Psu) / 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 ...Bacteriophage P4, Psu, polarity suppression protein / Phage polarity suppression protein (Psu) / 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
ADENOSINE-5'-TRIPHOSPHATE / Polarity suppression protein / Transcription termination factor Rho
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Enterobacteria phage P4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGjorgjevikj, D. / Wahl, M.C. / Hilal, T. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)RTG 2473-1 Germany
CitationJournal: Nat Commun / Year: 2025
Title: The Psu protein of phage satellite P4 inhibits transcription termination factor ρ by forced hyper-oligomerization.
Authors: Daniela Gjorgjevikj / Naveen Kumar / Bing Wang / Tarek Hilal / Nelly Said / Bernhard Loll / Irina Artsimovitch / Ranjan Sen / Markus C Wahl /
Abstract: Many bacteriophages modulate host transcription to favor expression of their own genomes. Phage satellite P4 polarity suppression protein, Psu, a building block of the viral capsid, inhibits ...Many bacteriophages modulate host transcription to favor expression of their own genomes. Phage satellite P4 polarity suppression protein, Psu, a building block of the viral capsid, inhibits hexameric transcription termination factor, ρ, by presently unknown mechanisms. Our cryogenic electron microscopy structures of ρ-Psu complexes show that Psu dimers clamp two inactive, open ρ rings and promote their expansion to higher-oligomeric states. ATPase, nucleotide binding and nucleic acid binding studies revealed that Psu hinders ρ ring closure and traps nucleotides in their binding pockets on ρ. Structure-guided mutagenesis in combination with growth, pull-down, and termination assays further delineated the functional ρ-Psu interfaces in vivo. Bioinformatic analyses revealed that Psu is associated with a wide variety of phage defense systems across Enterobacteriaceae, suggesting that Psu may regulate expression of anti-phage genes. Our findings show that modulation of the ρ oligomeric state via diverse strategies is a pervasive gene regulatory principle in bacteria.
History
DepositionAug 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Transcription termination factor Rho
D: Transcription termination factor Rho
E: Transcription termination factor Rho
J: Transcription termination factor Rho
K: Transcription termination factor Rho
L: Transcription termination factor Rho
M: Transcription termination factor Rho
O: Transcription termination factor Rho
c: Polarity suppression protein
d: Polarity suppression protein
e: Polarity suppression protein
f: Polarity suppression protein
g: Polarity suppression protein
h: Polarity suppression protein
i: Polarity suppression protein
j: Polarity suppression protein
k: Polarity suppression protein
l: Polarity suppression protein
B: Transcription termination factor Rho
G: Transcription termination factor Rho
N: Transcription termination factor Rho
F: Transcription termination factor Rho
hetero molecules


Theoretical massNumber of molelcules
Total (without water)785,15046
Polymers778,77322
Non-polymers6,37824
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Transcription termination factor Rho / ATP-dependent helicase Rho


Mass: 47070.168 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rho, nitA, psuA, rnsC, sbaA, tsu, b3783, JW3756 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AG30, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein
Polarity suppression protein / Amber mutation-suppressing protein


Mass: 21393.064 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P4 (virus) / Gene: psu / Production host: Escherichia coli (E. coli) / References: UniProt: P05460
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of E. coli transcription termination factor Rho with ATP and P4 polarity suppression protein PsuCOMPLEX#1-#20MULTIPLE SOURCES
2Transcription termination factor RhoCOMPLEX1RECOMBINANT
3Polarity suppression proteinCOMPLEX1RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Enterobacteria phage P4 (virus)10680
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 40.77 sec. / Electron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6409

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4particle selection
2EPU3.6image acquisition
4cryoSPARC4.4CTF correction
9cryoSPARC4.4initial Euler assignment
10cryoSPARC4.4final Euler assignment
12cryoSPARC4.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 966398
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17296 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 38
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00255540
ELECTRON MICROSCOPYf_angle_d0.46174928
ELECTRON MICROSCOPYf_dihedral_angle_d12.24121648
ELECTRON MICROSCOPYf_chiral_restr0.0398454
ELECTRON MICROSCOPYf_plane_restr0.0039770

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