+Open data
-Basic information
Entry | Database: PDB / ID: 8ftm | ||||||
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Title | Setx-ssRNA-ADP-SO4 complex | ||||||
Components |
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Keywords | TRANSCRIPTION/RNA / Helicase / TRANSCRIPTION-RNA complex / DNA repair / RNA-DNA hybrid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chaetomium thermophilum (fungus) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Williams, R.S. / Appel, C.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ftm.cif.gz | 725.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ftm.ent.gz | 498.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ftm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/8ftm ftp://data.pdbj.org/pub/pdb/validation_reports/ft/8ftm | HTTPS FTP |
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-Related structure data
Related structure data | 8fthC 8ftkC 5mznS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.951843143009, 0.0623091131356, 0.300186950962), (-0.055813690372, -0.997985166035, 0.0301735039531), (0.301462208369, 0.0119659013036, 0.953403038663)Vector: 47. ...NCS oper: (Code: given Matrix: (-0.951843143009, 0.0623091131356, 0.300186950962), Vector: |
-Components
#1: Protein | Mass: 88990.016 Da / Num. of mol.: 2 / Fragment: helicase domain (UNP residues 1087-1878) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0012480 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S163, DNA helicase #2: RNA chain | Mass: 4547.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) #3: Chemical | ChemComp-ADP / | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.66 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 200 mM sodium sulfate, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 37676 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 70.66 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.121 / Net I/σ(I): 11.42 |
Reflection shell | Resolution: 3→3.05 Å / Rmerge(I) obs: 0.725 / Num. unique obs: 1866 / CC1/2: 0.872 / CC star: 0.965 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5MZN Resolution: 3.01→44.54 Å / SU ML: 0.4288 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.0094 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.01→44.54 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 2.39248237802 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 33.5372106399 Å / Origin y: -36.9176532054 Å / Origin z: 30.2153049278 Å
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Refinement TLS group | Selection details: all |