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- EMDB-58425: Mycobacterium tuberculosis transcription termination factor Rho i... -

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Basic information

Entry
Database: EMDB / ID: EMD-58425
TitleMycobacterium tuberculosis transcription termination factor Rho in complex with an RNA substrate bound to the secondary binding site and the ATP analogue ADP-BeF3
Map dataMycobacterium tuberculosis transcription termination factor Rho in complex with RNA ligand bound at the secondary binding site and the ATP analogues ADP-BeF3.
Sample
  • Complex: Mycobacterium tuberculosis transcription termination factor Rho in complex with RNA ligand and ATP analogue ADP-BeF3
    • Protein or peptide: Transcription termination factor Rho
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
KeywordsTermination factor Rho / Mycobacterium tuberculosis / 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 / 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 / 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 speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWeixlbaumer A / Saint-Andre C
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0017 France
CitationJournal: To Be Published
Title: Mycobacterium tuberculosis transcription termination factor Rho in complex with an RNA substrate bound to the primary binding site and the ATP analogue ADP-BeF3
Authors: Weixlbaumer A / Saint-Andre C
History
DepositionJun 5, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58425.png

Downloads & links

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Map

FileDownload / File: emd_58425.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycobacterium tuberculosis transcription termination factor Rho in complex with RNA ligand bound at the secondary binding site and the ATP analogues ADP-BeF3.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 262.44 Å		0.73 Å/pix.
x 360 pix.
= 262.44 Å		0.73 Å/pix.
x 360 pix.
= 262.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.11885013 - 0.25560725
Average (Standard dev.)0.0004709162 (±0.008917962)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 262.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map of Mycobacterium tuberculosis transcription termination factor Rho...

Fileemd_58425_half_map_1.map
AnnotationHalf-map of Mycobacterium tuberculosis transcription termination factor Rho in complex with RNA ligand bound at the secondary binding site and the ATP analogues ADP-BeF3.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of Mycobacterium tuberculosis transcription termination factor Rho...

Fileemd_58425_half_map_2.map
AnnotationHalf-map of Mycobacterium tuberculosis transcription termination factor Rho in complex with RNA ligand bound at the secondary binding site and the ATP analogues ADP-BeF3.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium tuberculosis transcription termination factor Rho i...

EntireName: Mycobacterium tuberculosis transcription termination factor Rho in complex with RNA ligand and ATP analogue ADP-BeF3
Components
  • Complex: Mycobacterium tuberculosis transcription termination factor Rho in complex with RNA ligand and ATP analogue ADP-BeF3
    • Protein or peptide: Transcription termination factor Rho
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: Mycobacterium tuberculosis transcription termination factor Rho i...

SupramoleculeName: Mycobacterium tuberculosis transcription termination factor Rho in complex with RNA ligand and ATP analogue ADP-BeF3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (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
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 65.223371 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTDTDLITAG ESTDGKPSDA AATDPPDLNA DEPAGSLATM VLPELRALAN RAGVKGTSGM RKNELIAAIE EIRRQANGAP AVDRSAQEH DKGDRPPSSE APATQGEQTP TEQIDSQSQQ VRPERRSATR EAGPSGSGER AGTAADDTDN RQGGQQDAKT E ERGTDAGG ...String:
MTDTDLITAG ESTDGKPSDA AATDPPDLNA DEPAGSLATM VLPELRALAN RAGVKGTSGM RKNELIAAIE EIRRQANGAP AVDRSAQEH DKGDRPPSSE APATQGEQTP TEQIDSQSQQ VRPERRSATR EAGPSGSGER AGTAADDTDN RQGGQQDAKT E ERGTDAGG DQGGDQQASG GQQARGDEDG EARQGRRGRR FRDRRRRGER SGDGAEAELR EDDVVQPVAG ILDVLDNYAF VR TSGYLPG PHDVYVSMNM VRKNGMRRGD AVTGAVRVPK EGEQPNQRQK FNPLVRLDSI NGGSVEDAKK RPEFGKLTPL YPN QRLRLE TSTERLTTRV IDLIMPIGKG QRALIVSPPK AGKTTILQDI ANAITRNNPE CHLMVVLVDE RPEEVTDMQR SVKG EVIAS TFDRPPSDHT SVAELAIERA KRLVEQGKDV VVLLDSITRL GRAYNNASPA SGRILSGGVD STALYPPKRF LGAAR NIEE GGSLTIIATA MVETGSTGDT VIFEEFKGTG NAELKLDRKI AERRVFPAVD VNPSGTRKDE LLLSPDEFAI VHKLRR VLS GLDSHQAIDL LMSQLRKTKN NYEFLVQVSK TTPGSMDSD

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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 22095 / Average exposure time: 2.0 sec. / Average electron dose: 39.18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7oqh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 37145
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7oqh


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-31hy:
Mycobacterium tuberculosis transcription termination factor Rho in complex with an RNA substrate bound to the secondary binding site and the ATP analogue ADP-BeF3

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