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- PDB-8ftm: Setx-ssRNA-ADP-SO4 complex -

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Basic information

Entry
Database: PDB / ID: 8ftm
TitleSetx-ssRNA-ADP-SO4 complex
Components
  • 5'-3' RNA helicase-like protein
  • RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsTRANSCRIPTION/RNA / Helicase / TRANSCRIPTION-RNA complex / 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 / nuclear body / nucleotide 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 / RNA / RNA (> 10) / 5'-3' RNA helicase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 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

Downloads & links

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Assembly

Deposited unit
A: 5'-3' RNA helicase-like protein
B: 5'-3' RNA helicase-like protein
C: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
D: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,36714
Polymers187,0754
Non-polymers1,29210
Water1086
1
A: 5'-3' RNA helicase-like protein
C: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2536
Polymers93,5382
Non-polymers7154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-3' RNA helicase-like protein
D: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1148
Polymers93,5382
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.705, 107.323, 162.029
Angle α, β, γ (deg.)90.000, 99.640, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1102 through 1123 or resid 1132 through 1857 or resid 2002 through 2004))
d_2ens_1(chain "B" and ((resid 1102 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGGLYA1 - 22
d_12ens_1CYSLYSA26 - 714
d_13ens_1SO4SO4C
d_14ens_1SO4SO4D
d_15ens_1SO4SO4E
d_21ens_1ARGLEUF4 - 256
d_22ens_1LYSLEUF260 - 324
d_23ens_1ARGALAF333 - 389
d_24ens_1GLYLYSF394 - 729
d_25ens_1SO4SO4J
d_26ens_1SO4SO4K
d_27ens_1SO4SO4L

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), (-0.055813690372, -0.997985166035, 0.0301735039531), (0.301462208369, 0.0119659013036, 0.953403038663)
Vector: 47.753163876, -74.4174228644, -79.2357412542)

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Components

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


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 RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 4547.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: 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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 200 mM sodium sulfate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.725 / Num. unique obs: 1866 / CC1/2: 0.872 / CC star: 0.965

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5MZN

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
RfactorNum. reflection% reflection
Rfree0.251 1999 5.33 %
Rwork0.2117 35472 -
obs0.2139 37471 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.08 Å2
Refinement stepCycle: LAST / Resolution: 3.01→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11394 370 72 6 11842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212060
X-RAY DIFFRACTIONf_angle_d0.523916365
X-RAY DIFFRACTIONf_chiral_restr0.04031850
X-RAY DIFFRACTIONf_plane_restr0.00442052
X-RAY DIFFRACTIONf_dihedral_angle_d12.98744576
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.39248237802 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.080.36221290.31362391X-RAY DIFFRACTION93.51
3.08-3.170.3311470.3122518X-RAY DIFFRACTION98.19
3.17-3.260.33111390.28612533X-RAY DIFFRACTION98.93
3.26-3.370.31781440.26082565X-RAY DIFFRACTION99.05
3.37-3.490.32121450.24882509X-RAY DIFFRACTION98.92
3.49-3.630.30311430.23522536X-RAY DIFFRACTION98.86
3.63-3.790.28731470.24382579X-RAY DIFFRACTION99.02
3.79-3.990.26241420.2312493X-RAY DIFFRACTION98.62
3.99-4.240.23911330.19952479X-RAY DIFFRACTION96.28
4.24-4.570.25221480.16442579X-RAY DIFFRACTION99.49
4.57-5.030.17861460.16332572X-RAY DIFFRACTION99.63
5.03-5.750.24311480.19522574X-RAY DIFFRACTION99.45
5.75-7.240.2371440.21892583X-RAY DIFFRACTION99.02
7.24-44.540.20061440.18122561X-RAY DIFFRACTION96.88
Refinement TLS params.Method: refined / Origin x: 33.5372106399 Å / Origin y: -36.9176532054 Å / Origin z: 30.2153049278 Å
111213212223313233
T0.509688209314 Å2-0.0236388187141 Å2-0.0509014705705 Å2-0.372553153223 Å2-0.0100389083958 Å2--0.444219966588 Å2
L0.216062998469 °20.0228450055898 °2-0.247984564955 °2-0.209912178603 °20.12644520072 °2--0.849531811849 °2
S-0.00314620709059 Å °-0.0831010860391 Å °0.0659895803606 Å °0.0636383906536 Å °-0.0377883788827 Å °0.0287179413161 Å °-0.108069575026 Å °0.0971365375437 Å °0.0315099444451 Å °
Refinement TLS groupSelection details: all

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