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- PDB-6uv3: Crystal structure of the core domain of RNA helicase DDX17 with R... -

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Basic information

Entry
Database: PDB / ID: 6uv3
TitleCrystal structure of the core domain of RNA helicase DDX17 with RNA pri-125a-oligo2
Components
  • 125a-oligo2
  • Probable ATP-dependent RNA helicase DDX17
KeywordsRNA BINDING PROTEIN/RNA / DEAD-box ATPase / RNA helicase / RNA binding / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of skeletal muscle cell differentiation / alternative mRNA splicing, via spliceosome / miRNA metabolic process / ATP-dependent activity, acting on RNA / regulatory ncRNA-mediated gene silencing / myoblast differentiation / regulation of alternative mRNA splicing, via spliceosome / immune system process / androgen receptor signaling pathway / epithelial to mesenchymal transition ...regulation of skeletal muscle cell differentiation / alternative mRNA splicing, via spliceosome / miRNA metabolic process / ATP-dependent activity, acting on RNA / regulatory ncRNA-mediated gene silencing / myoblast differentiation / regulation of alternative mRNA splicing, via spliceosome / immune system process / androgen receptor signaling pathway / epithelial to mesenchymal transition / intracellular estrogen receptor signaling pathway / RNA processing / ribonucleoprotein complex binding / SUMOylation of transcription cofactors / mRNA 3'-UTR binding / rRNA processing / defense response to virus / RNA helicase activity / transcription coactivator activity / RNA helicase / nuclear speck / ribonucleoprotein complex / nucleolus / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
DEAD box protein 17, ATP-binding domain / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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. ...DEAD box protein 17, ATP-binding domain / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / RNA / Probable ATP-dependent RNA helicase DDX17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.597 Å
AuthorsNgo, T.D. / Partin, A.C. / Nam, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Cell Rep / Year: 2019
Title: RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis.
Authors: Ngo, T.D. / Partin, A.C. / Nam, Y.
History
DepositionNov 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX17
B: 125a-oligo2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9735
Polymers54,4562
Non-polymers5183
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-34 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.327, 112.327, 99.094
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-684-

HOH

21A-953-

HOH

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein Probable ATP-dependent RNA helicase DDX17 / DEAD box protein 17 / DEAD box protein p72 / DEAD box protein p82 / RNA-dependent helicase p72


Mass: 51295.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92841, RNA helicase
#2: RNA chain 125a-oligo2


Mass: 3159.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 393 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 40% PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.597→50 Å / Num. obs: 95681 / % possible obs: 99.9 % / Redundancy: 19.4 % / Rrim(I) all: 0.103 / Net I/σ(I): 46.5
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 4748 / Rrim(I) all: 1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DDX17-rU10

Resolution: 1.597→36.768 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 1964 2.09 %
Rwork0.1749 91786 -
obs0.1754 93750 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.51 Å2 / Biso mean: 26.5409 Å2 / Biso min: 12.64 Å2
Refinement stepCycle: final / Resolution: 1.597→36.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3415 128 32 390 3965
Biso mean--19.28 35.35 -
Num. residues----433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5971-1.63710.19631330.2037609492
1.6371-1.68140.20091310.1906625894
1.6814-1.73080.20091380.1835628695
1.7308-1.78670.20641330.178640497
1.7867-1.85060.17761410.176651898
1.8506-1.92460.20021370.1778648398
1.9246-2.01220.20241410.1716660999
2.0122-2.11830.18051450.168663999
2.1183-2.2510.20211390.17026665100
2.251-2.42480.17161430.16986680100
2.4248-2.66870.18741440.17226691100
2.6687-3.05470.18921460.17916723100
3.0547-3.8480.22431400.16816778100
3.848-36.7680.19591530.17916958100

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