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- PDB-8szq: Cat DHX9 bound to ADP -

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Basic information

Entry
Database: PDB / ID: 8szq
TitleCat DHX9 bound to ADP
ComponentsRNA helicase
KeywordsHYDROLASE / DExH-box / ADP / 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 / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation ...DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / 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 domain / DEAD/DEAH box helicase / 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
ADENOSINE-5'-DIPHOSPHATE / RNA helicase
Similarity search - Component
Biological speciesFelis catus (domestic cat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.711 Å
AuthorsLee, Y.-T. / Sickmier, E.A. / Grigoriu, S. / Boriack-Sjodin, P.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Crystal structures of the DExH-box RNA helicase DHX9.
Authors: Lee, Y.T. / Sickmier, E.A. / Grigoriu, S. / Castro, J. / Boriack-Sjodin, P.A.
History
DepositionMay 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,13616
Polymers114,6051
Non-polymers1,53015
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.010, 86.010, 348.850
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


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, 109 molecules

#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
#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


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 56.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.15 M Ammonium sulfate, 0.1 M TRIS pH 8, 19% (w/v) PEG 4000; 5 mM ADP 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: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95364 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.71→48.17 Å / Num. obs: 36693 / % possible obs: 99.8 % / Redundancy: 26.1 % / CC1/2: 1 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.025 / Rrim(I) all: 0.129 / Χ2: 0.99 / Net I/σ(I): 23.1 / Num. measured all: 959448
Reflection shellResolution: 2.71→2.83 Å / % possible obs: 98.2 % / Redundancy: 25.5 % / Rmerge(I) obs: 1.519 / Num. measured all: 110071 / Num. unique obs: 4317 / CC1/2: 0.791 / Rpim(I) all: 0.299 / Rrim(I) all: 1.549 / Χ2: 0.88 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.711→48.17 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.515 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.632 / ESU R Free: 0.339
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 1822 4.966 %RANDOM
Rwork0.2256 34868 --
all0.228 ---
obs-36690 99.712 %-
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: 71.008 Å2
Baniso -1Baniso -2Baniso -3
1-1.814 Å2-0 Å20 Å2
2--1.814 Å2-0 Å2
3----3.627 Å2
Refinement stepCycle: LAST / Resolution: 2.711→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6831 0 88 94 7013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0127062
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166738
X-RAY DIFFRACTIONr_angle_refined_deg0.7081.6499583
X-RAY DIFFRACTIONr_angle_other_deg0.2521.56315523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3845858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.019547
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg051
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.971101215
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.75910322
X-RAY DIFFRACTIONr_chiral_restr0.0360.21093
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021575
X-RAY DIFFRACTIONr_nbd_refined0.1780.21449
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.26260
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23461
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.23550
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2157
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0860.27
X-RAY DIFFRACTIONr_nbd_other0.1270.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2180.22
X-RAY DIFFRACTIONr_mcbond_it2.0437.1273441
X-RAY DIFFRACTIONr_mcbond_other2.0427.1273441
X-RAY DIFFRACTIONr_mcangle_it3.56412.8134296
X-RAY DIFFRACTIONr_mcangle_other3.56412.8154297
X-RAY DIFFRACTIONr_scbond_it1.8917.4853621
X-RAY DIFFRACTIONr_scbond_other1.8917.4853622
X-RAY DIFFRACTIONr_scangle_it3.36413.6845287
X-RAY DIFFRACTIONr_scangle_other3.36313.6845288
X-RAY DIFFRACTIONr_lrange_it6.22866.3697692
X-RAY DIFFRACTIONr_lrange_other6.22666.3817687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.711-2.7810.3971240.3372461X-RAY DIFFRACTION96.8528
2.781-2.8570.3791330.3112433X-RAY DIFFRACTION99.9221
2.857-2.940.3281320.2982365X-RAY DIFFRACTION99.96
2.94-3.030.3441110.2892346X-RAY DIFFRACTION100
3.03-3.1290.3161140.2842263X-RAY DIFFRACTION100
3.129-3.2380.3491150.2782189X-RAY DIFFRACTION100
3.238-3.360.311090.2652120X-RAY DIFFRACTION100
3.36-3.4960.2781090.2492035X-RAY DIFFRACTION100
3.496-3.6510.2681000.2391972X-RAY DIFFRACTION100
3.651-3.8280.2571040.2281890X-RAY DIFFRACTION100
3.828-4.0340.2621070.2111775X-RAY DIFFRACTION100
4.034-4.2770.255720.21738X-RAY DIFFRACTION100
4.277-4.5690.217740.1981631X-RAY DIFFRACTION100
4.569-4.9320.208920.1781498X-RAY DIFFRACTION99.9371
4.932-5.3970.285660.2061411X-RAY DIFFRACTION100
5.397-6.0240.283540.2171299X-RAY DIFFRACTION100
6.024-6.9380.265740.2131131X-RAY DIFFRACTION100
6.938-8.4540.212540.171995X-RAY DIFFRACTION100
8.454-11.7760.24520.156792X-RAY DIFFRACTION100
11.776-48.170.335260.291524X-RAY DIFFRACTION99.8185

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