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- EMDB-34999: Thermus thermophilus transcription termination factor Rho bound w... -

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Basic information

Entry
Database: EMDB / ID: EMD-34999
TitleThermus thermophilus transcription termination factor Rho bound with ADP-BeF3
Map data
Sample
  • Complex: Transcription termination factor Rho
    • Protein or peptide: Transcription termination factor Rho
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
KeywordsTranscription termination / ATP-dependent RNA/DNA helicase/translocase / 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
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 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding 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 / 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 speciesThermus thermophilus HB8 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMurayama Y / Ehara H / Sekine S
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17K15082 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05690 Japan
CitationJournal: Sci Adv / Year: 2023
Title: Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from .
Authors: Yuko Murayama / Haruhiko Ehara / Mari Aoki / Mie Goto / Takeshi Yokoyama / Shun-Ichi Sekine /
Abstract: Transcription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, transcription termination is mediated by the ...Transcription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, transcription termination is mediated by the adenosine triphosphate-dependent RNA translocase/helicase Rho, which causes RNA/DNA dissociation from the RNAP elongation complex (EC). However, the structural basis of the interplay between Rho and RNAP remains obscure. Here, we report the cryo-electron microscopy structure of the RNAP EC engaged with Rho. The Rho hexamer binds RNAP through the carboxyl-terminal domains, which surround the RNA exit site of RNAP, directing the nascent RNA seamlessly from the RNA exit to its central channel. The β-flap tip at the RNA exit is critical for the Rho-dependent RNA release, and its deletion causes an alternative Rho-RNAP binding mode, which is irrelevant to termination. The Rho binding site overlaps with the binding sites of other macromolecules, such as ribosomes, providing a general basis of gene regulation.
History
DepositionDec 19, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34999.png

Downloads & links

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Map

FileDownload / File: emd_34999.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.019059736 - 0.044403445
Average (Standard dev.)0.000009368875 (±0.0012113045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34999_half_map_1.map
Projections & Slices
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Slices (1/2)
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Half map: #2

Fileemd_34999_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Transcription termination factor Rho

EntireName: Transcription termination factor Rho
Components
  • Complex: Transcription termination factor Rho
    • Protein or peptide: Transcription termination factor Rho
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: Transcription termination factor Rho

SupramoleculeName: Transcription termination factor Rho / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)

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Macromolecule #1: Transcription termination factor Rho

MacromoleculeName: Transcription termination factor Rho / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 47.99627 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPMRRKETLQ ETPLTYQELA SKILPELHLL AQEAGIEGYK RMKKDQLIMA LLERQTQGEG LRLVKGYLEI SQDGYGFLTE NLHNLESRV AIVSAGLIKQ YALRAGDYVV GQARPPRENE RYATLLKVEA VNNLDPEAAK NRPRFDELTP QFPDRQIRLE T TPDELSTR ...String:
GPMRRKETLQ ETPLTYQELA SKILPELHLL AQEAGIEGYK RMKKDQLIMA LLERQTQGEG LRLVKGYLEI SQDGYGFLTE NLHNLESRV AIVSAGLIKQ YALRAGDYVV GQARPPRENE RYATLLKVEA VNNLDPEAAK NRPRFDELTP QFPDRQIRLE T TPDELSTR VIDLLAPIGR GQRGLIVAPP KAGKTTLLKK IANAVLKNEP DIKVIVLLID ERPEEVTDFR ESVQGAEVIA ST FDEPPQN HIRVAEFVHE RAKRIVEEGG HVMILLDSIT RLARANNLVT PPTGRTLSGG LDSAALYFPK RFLGAARNIR GGG SLTILA TALVETGSRM DDVIFEEFKG TGNMELHLSR RLEERRIFPA IDILKSGTRR EELLLGEEVT HKMWLLRKVL ADMD PAEAM EMLLARLART KNNKEFLASL AAR

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: 6 / 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: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5jji

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 205226
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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