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- EMDB-17640: Rho P167L-ATPgS-Psu complex I -

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Basic information

Entry
Database: EMDB / ID: EMD-17640
TitleRho P167L-ATPgS-Psu complex I
Map data
Sample
  • Complex: Complex of E. coli transcription termination factor Rho P167L variant with the ATP analog, ATPgammaS and P4 polarity suppression protein Psu
    • Complex: Transcription termination factor Rho
      • Protein or peptide: Transcription termination factor Rho
    • Complex: Polarity suppression protein
      • Protein or peptide: Polarity suppression protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsTranscription 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 / 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
Polarity suppression protein / Transcription termination factor Rho
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Enterobacteria phage P4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGjorgjevikj D / Wahl MC / Hilal T / Loll B
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)RTG 2473-1 Germany
CitationJournal: To Be Published
Title: Rho P167L-ATPgS-Psu complex I
Authors: Gjorgjevikj D / Wahl MC / Hilal T / Loll B
History
DepositionJun 15, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17640.png

Downloads & links

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Map

FileDownload / File: emd_17640.map.gz / Format: CCP4 / Size: 343 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 448 pix.
= 372.736 Å		0.83 Å/pix.
x 448 pix.
= 372.736 Å		0.83 Å/pix.
x 448 pix.
= 372.736 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.0 - 2.2887056
Average (Standard dev.)0.010164511 (±0.057167858)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 372.73602 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_17640_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17640_half_map_2.map
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 E. coli transcription termination factor Rho P167L var...

EntireName: Complex of E. coli transcription termination factor Rho P167L variant with the ATP analog, ATPgammaS and P4 polarity suppression protein Psu
Components
  • Complex: Complex of E. coli transcription termination factor Rho P167L variant with the ATP analog, ATPgammaS and P4 polarity suppression protein Psu
    • Complex: Transcription termination factor Rho
      • Protein or peptide: Transcription termination factor Rho
    • Complex: Polarity suppression protein
      • Protein or peptide: Polarity suppression protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of E. coli transcription termination factor Rho P167L var...

SupramoleculeName: Complex of E. coli transcription termination factor Rho P167L variant with the ATP analog, ATPgammaS and P4 polarity suppression protein Psu
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2

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Supramolecule #2: Transcription termination factor Rho

SupramoleculeName: Transcription termination factor Rho / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Polarity suppression protein

SupramoleculeName: Polarity suppression protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Enterobacteria phage P4 (virus)

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Macromolecule #1: Transcription termination factor Rho

MacromoleculeName: Transcription termination factor Rho / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 47.086211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNLTELKNTP VSELITLGEN MGLENLARMR KQDIIFAILK QHAKSGEDIF GDGVLEILQD GFGFLRSADS SYLAGPDDIY VSPSQIRRF NLRTGDTISG KIRPPKEGER YFALLKVNEV NFDKPENARN KILFENLTPL HANSRLRMER GNGSTEDLTA R VLDLASLI ...String:
MNLTELKNTP VSELITLGEN MGLENLARMR KQDIIFAILK QHAKSGEDIF GDGVLEILQD GFGFLRSADS SYLAGPDDIY VSPSQIRRF NLRTGDTISG KIRPPKEGER YFALLKVNEV NFDKPENARN KILFENLTPL HANSRLRMER GNGSTEDLTA R VLDLASLI GRGQRGLIVA PPKAGKTMLL QNIAQSIAYN HPDCVLMVLL IDERPEEVTE MQRLVKGEVV ASTFDEPASR HV QVAEMVI EKAKRLVEHK KDVIILLDSI TRLARAYNTV VPASGKVLTG GVDANALHRP KRFFGAARNV EEGGSLTIIA TAL IDTGSK MDEVIYEEFK GTGNMELHLS RKIAEKRVFP AIDYNRSGTR KEELLTTQEE LQKMWILRKI IHPMGEIDAM EFLI NKLAM TKTNDDFFEM MKRS

UniProtKB: Transcription termination factor Rho

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Macromolecule #2: Polarity suppression protein

MacromoleculeName: Polarity suppression protein / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage P4 (virus)
Molecular weightTheoretical: 21.393064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MESTALQQAF DTCQNNKAAW LQRKNELAAA EQEYLRLLSG EGRNVSRLDE LRNIIEVRKW QVNQAAGRYI RSHEAVQHIS IRDRLNDFM QQHGTALAAA LAPELMGYSE LTAIARNCAI QRATDALREA LLSWLAKGEK INYSAQDSDI LTTIGFRPDV A SVDDSREK FTPAQNMIFS RKSAQLASRQ SV

UniProtKB: Polarity suppression protein

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 12 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration4.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: NITROGEN / 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: 2766 / Average exposure time: 40.57 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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

Particle selectionNumber selected: 823078
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.0) / Number images used: 273935
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. v3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v3.3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1pv4

source_name: PDB, initial_model_type: experimental model

3rx6

source_name: PDB, initial_model_type: experimental model
DetailsCrystal 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.
RefinementSpace: REAL / Target criteria: Cross-correlation coefficient
Output model

PDB-8pex:
Rho P167L-ATPgS-Psu complex I

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