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- PDB-8fth: Chaetomium thermophilum SETX - NPPC internal deletion -

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Basic information

Entry
Database: PDB / ID: 8fth
TitleChaetomium thermophilum SETX - NPPC internal deletion
Components5'-3' RNA helicase-like protein
KeywordsTRANSCRIPTION / Helicase / DNA repair / RNA-DNA hybrid
Function / homology
Function and homology information


transcription termination site sequence-specific DNA binding / termination of RNA polymerase II transcription / helicase activity / chromosome / nuclear body / hydrolase activity / ATP binding
Similarity search - Function
Helicase Sen1, N-terminal / : / SEN1 N terminal / Helicase SEN1 beta-barrel domain / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 5'-3' RNA helicase-like protein
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsWilliams, R.S. / Appel, C.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES102765 United States
CitationJournal: Mol Cell / Year: 2023
Title: Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2.
Authors: C Denise Appel / Oya Bermek / Venkata P Dandey / Makayla Wood / Elizabeth Viverette / Jason G Williams / Jonathan Bouvette / Amanda A Riccio / Juno M Krahn / Mario J Borgnia / R Scott Williams /
Abstract: The senataxin (SETX, Sen1 in yeasts) RNA-DNA hybrid resolving helicase regulates multiple nuclear transactions, including DNA replication, transcription, and DNA repair, but the molecular basis for ...The senataxin (SETX, Sen1 in yeasts) RNA-DNA hybrid resolving helicase regulates multiple nuclear transactions, including DNA replication, transcription, and DNA repair, but the molecular basis for Sen1 activities is ill defined. Here, Sen1 cryoelectron microscopy (cryo-EM) reconstructions reveal an elongated inchworm-like architecture. Sen1 is composed of an amino terminal helical repeat Sen1 N-terminal (Sen1N) regulatory domain that is flexibly linked to its C-terminal SF1B helicase motor core (Sen1) via an intrinsically disordered tether. In an autoinhibited state, the Sen1 domain regulates substrate engagement by promoting occlusion of the RNA substrate-binding cleft. The X-ray structure of an activated Sen1 engaging single-stranded RNA and ADP-SO shows that the enzyme encircles RNA and implicates a single-nucleotide power stroke in the Sen1 RNA translocation mechanism. Together, our data unveil dynamic protein-protein and protein-RNA interfaces underpinning helicase regulation and inactivation of human SETX activity by RNA-binding-deficient mutants in ataxia with oculomotor apraxia 2 neurodegenerative disease.
History
DepositionJan 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-3' RNA helicase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,3582
Polymers190,9311
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein 5'-3' RNA helicase-like protein / SETX


Mass: 190931.109 Da / Num. of mol.: 1
Fragment: UNP residues 1-903,1090-1858),UNP residues 1-903,1090-1858)
Source method: isolated from a genetically manipulated source
Details: engineered fragment: internal deletion and C-terminal truncation,engineered fragment: internal deletion and C-terminal truncation
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0012480 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: G0S163, DNA helicase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

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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

ComponentName: Chaemtomium thermophilum SETX in complex with ADP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Chaetomium thermophilum (fungus)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293F
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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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: 2700 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
10cryoSPARC3.3.2initial Euler assignment
11cryoSPARC3.3.2final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 471395 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 51.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0089945
ELECTRON MICROSCOPYf_angle_d1.25613451
ELECTRON MICROSCOPYf_dihedral_angle_d5.4211352
ELECTRON MICROSCOPYf_chiral_restr0.0521550
ELECTRON MICROSCOPYf_plane_restr0.0081716

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