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- PDB-8pey: Rho P167L-ATPgS-Psu complex II -

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Basic information

Entry
Database: PDB / ID: 8pey
TitleRho P167L-ATPgS-Psu complex II
Components
  • Polarity suppression protein
  • Transcription termination factor Rho
KeywordsGENE REGULATION / Transcription termination / Phage inhibitor
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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / 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 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: To Be Published
Title: Rho P167L-ATPgS-Psu complex II
Authors: Gjorgjevikj, D. / Wahl, M.C. / Hilal, T. / Loll, B.
History
DepositionJun 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription termination factor Rho
B: Transcription termination factor Rho
C: Transcription termination factor Rho
D: Transcription termination factor Rho
E: Transcription termination factor Rho
F: Transcription termination factor Rho
G: Transcription termination factor Rho
I: Transcription termination factor Rho
J: Transcription termination factor Rho
K: Transcription termination factor Rho
L: Transcription termination factor Rho
M: Transcription termination factor Rho
N: Transcription termination factor Rho
a: Polarity suppression protein
b: Polarity suppression protein
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)832,62247
Polymers826,05123
Non-polymers6,57124
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: 47086.211 Da / Num. of mol.: 13
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-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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 P167L variant with the ATP analog, ATPgammaS and P4 polarity suppression protein PsuCOMPLEX#1-#20MULTIPLE SOURCES
2Transcription termination factor RhoCOMPLEX#11RECOMBINANT
3Polarity suppression proteinCOMPLEX#21RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Enterobacteria phage P4 (virus)10680
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: NITROGEN / 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 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: 40.57 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2766

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv3.2.0particle selection
2EPU2.9image acquisition
4cryoSPARCv3.2.0CTF correction
7Coot0.9.6model fitting
9PHENIX1.20_4459model refinement
10cryoSPARCv3.2.0initial Euler assignment
11cryoSPARCv3.3.0final Euler assignment
12cryoSPARCv3.3.0classification
13cryoSPARCv3.3.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 823078
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 317635 / Symmetry type: POINT
Atomic model buildingSpace: REAL / Target criteria: Cross-correlation coefficient
Details: Crystal structures of Rho (PDB ID: 1PV4) and Psu (PDB ID: 3RX6) were manually placed in the cryoEM reconstructions and each protomer was adjusted by rigid body fitting and segmental real- ...Details: Crystal structures of Rho (PDB ID: 1PV4) and Psu (PDB ID: 3RX6) were manually placed in the cryoEM reconstructions and each protomer was adjusted by rigid body fitting and segmental real-space refinement using Coot (version 0.9.6). The model was refined by iterative rounds of real space refinement in PHENIX (version 1.20_4459) and manual adjustment in Coot.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11PV4

1pv4

11PV41PDBexperimental model
23RX6

3rx6

13RX62PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 143.53 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002556765
ELECTRON MICROSCOPYf_angle_d0.603776575
ELECTRON MICROSCOPYf_chiral_restr0.04288687
ELECTRON MICROSCOPYf_plane_restr0.0049969
ELECTRON MICROSCOPYf_dihedral_angle_d5.66827826

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