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- PDB-8szs: Cat DHX9 bound to GDP -

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Basic information

Entry
Database: PDB / ID: 8szs
TitleCat DHX9 bound to GDP
ComponentsRNA helicaseHelicase
KeywordsHYDROLASE / DExH-box / RHA
Function / homology
Function and homology information


3'-5' DNA/RNA helicase activity / DNA-templated transcription termination / double-stranded RNA binding / RNA helicase activity / hydrolase activity / RNA helicase / ATP binding / nucleus
Similarity search - Function
DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / Double-stranded RNA binding motif / Double-stranded RNA binding motif ...DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / Double-stranded RNA binding motif / Double-stranded RNA binding motif / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / RNA helicase
Similarity search - Component
Biological speciesFelis catus (domestic cat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsLee, Y.-T. / Sickmier, E.A. / Boriack-Sjodin, P.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Slas Discov / Year: 2023
Title: Development of assays to support identification and characterization of modulators of DExH-box helicase DHX9.
Authors: Gotur, D. / Case, A. / Liu, J. / Sickmier, E.A. / Holt, N. / Knockenhauer, K.E. / Yao, S. / Lee, Y.T. / Copeland, R.A. / Buker, S.M. / Boriack-Sjodin, P.A.
History
DepositionMay 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,99329
Polymers114,6051
Non-polymers2,38728
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.110, 86.110, 347.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RNA helicase / Helicase


Mass: 114605.445 Da / Num. of mol.: 1 / Fragment: residues 151-1151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: DHX9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A337SGK2

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Non-polymers , 5 types, 322 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.15 M ammonium sulfate, 0.1 M Tris, pH 8.2, 15% w/v PEG4000; 5 mM GDP and 50 mM magnesium chloride in protein solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→48.03 Å / Num. obs: 53722 / % possible obs: 100 % / Redundancy: 26.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.029 / Rrim(I) all: 0.147 / Χ2: 0.99 / Net I/σ(I): 17.4 / Num. measured all: 1403168
Reflection shellResolution: 2.38→2.45 Å / % possible obs: 100 % / Redundancy: 24.2 % / Rmerge(I) obs: 1.542 / Num. measured all: 110689 / Num. unique obs: 4579 / CC1/2: 0.834 / Rpim(I) all: 0.317 / Rrim(I) all: 1.575 / Χ2: 0.88 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→48.03 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.538 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.242
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 2726 5.075 %RANDOM
Rwork0.2176 50991 --
all0.22 ---
obs-53717 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.881 Å2
Baniso -1Baniso -2Baniso -3
1-0.496 Å2-0 Å20 Å2
2--0.496 Å2-0 Å2
3----0.992 Å2
Refinement stepCycle: LAST / Resolution: 2.38→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6787 0 142 294 7223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0127092
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166812
X-RAY DIFFRACTIONr_angle_refined_deg0.7921.6529603
X-RAY DIFFRACTIONr_angle_other_deg0.2691.56415691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.625862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.044548
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.01251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.949101222
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.27710320
X-RAY DIFFRACTIONr_chiral_restr0.0390.21095
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021574
X-RAY DIFFRACTIONr_nbd_refined0.1910.21431
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.26238
X-RAY DIFFRACTIONr_nbtor_refined0.170.23441
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.23561
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2293
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.060.29
X-RAY DIFFRACTIONr_nbd_other0.1530.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.25
X-RAY DIFFRACTIONr_mcbond_it1.8685.2583430
X-RAY DIFFRACTIONr_mcbond_other1.8675.2583430
X-RAY DIFFRACTIONr_mcangle_it3.1269.4494283
X-RAY DIFFRACTIONr_mcangle_other3.1269.4494284
X-RAY DIFFRACTIONr_scbond_it2.0175.6613662
X-RAY DIFFRACTIONr_scbond_other2.0175.6613663
X-RAY DIFFRACTIONr_scangle_it3.5110.2865315
X-RAY DIFFRACTIONr_scangle_other3.5110.2865316
X-RAY DIFFRACTIONr_lrange_it6.10549.9537818
X-RAY DIFFRACTIONr_lrange_other6.09349.9867776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.4420.3461920.2813690X-RAY DIFFRACTION99.9742
2.442-2.5080.342180.2793541X-RAY DIFFRACTION100
2.508-2.5810.3291440.273540X-RAY DIFFRACTION99.9457
2.581-2.660.3481610.2693441X-RAY DIFFRACTION100
2.66-2.7470.2951950.2533286X-RAY DIFFRACTION100
2.747-2.8430.2961830.2413192X-RAY DIFFRACTION99.9704
2.843-2.950.2861520.2363112X-RAY DIFFRACTION99.9694
2.95-3.070.2831420.2383020X-RAY DIFFRACTION100
3.07-3.2060.261640.2382865X-RAY DIFFRACTION100
3.206-3.3620.2881430.2422736X-RAY DIFFRACTION100
3.362-3.5430.2771470.242624X-RAY DIFFRACTION100
3.543-3.7560.2951340.232496X-RAY DIFFRACTION100
3.756-4.0140.2341130.2052369X-RAY DIFFRACTION100
4.014-4.3330.2621230.1852212X-RAY DIFFRACTION100
4.333-4.7430.221290.1792015X-RAY DIFFRACTION100
4.743-5.2960.2541050.181862X-RAY DIFFRACTION100
5.296-6.1030.266860.2141681X-RAY DIFFRACTION100
6.103-7.4450.28890.1971417X-RAY DIFFRACTION100
7.445-10.4040.148600.1481162X-RAY DIFFRACTION100
10.404-48.030.27460.251730X-RAY DIFFRACTION100

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