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- PDB-6uv4: Crystal structure of the core domain of RNA helicase DDX17 with R... -

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Basic information

Entry
Database: PDB / ID: 6uv4
TitleCrystal structure of the core domain of RNA helicase DDX17 with RNA pri-18a-oligo1
Components
  • 18a_oligo1
  • 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 / ribonucleoprotein complex binding / RNA processing / estrogen receptor signaling pathway / 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 / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / 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. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / 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. ...DEAD box protein 17, ATP-binding domain / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / 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 / BERYLLIUM TRIFLUORIDE ION / RNA / Probable ATP-dependent RNA helicase DDX17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX17
C: 18a_oligo1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9195
Polymers54,4022
Non-polymers5183
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.504, 62.504, 231.196
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11C-9-

A

21C-9-

A

31A-609-

HOH

41A-936-

HOH

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Components

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Protein / RNA chain , 2 types, 2 molecules AC

#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 18a_oligo1


Mass: 3105.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 448 molecules

#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-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


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium acetate pH 4.6, 0.1M sodium chloride, 14% MDP, 10 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 52488 / % possible obs: 99.9 % / Redundancy: 22.9 % / CC1/2: 0.996 / Rrim(I) all: 0.168 / Net I/σ(I): 36.1
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 2555 / CC1/2: 0.55 / Rrim(I) all: 3.717

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DDX17_rU10

Resolution: 1.7→48.545 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.4
RfactorNum. reflection% reflection
Rfree0.204 2000 3.89 %
Rwork0.1725 --
obs0.1738 51398 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.37 Å2 / Biso mean: 18.0351 Å2 / Biso min: 3.69 Å2
Refinement stepCycle: final / Resolution: 1.7→48.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3404 144 32 445 4025
Biso mean--7.93 28.3 -
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 (%)
1.7-1.73260.24041150.2175284381
1.7326-1.77950.24541330.2119326993
1.7795-1.83180.2591400.2048346197
1.8318-1.8910.21411430.1959352599
1.891-1.95860.22951410.178350799
1.9586-2.0370.20631430.17183526100
2.037-2.12970.21681440.1693560100
2.1297-2.2420.2061450.16543587100
2.242-2.38240.221450.16193579100
2.3824-2.56640.19281450.15973585100
2.5664-2.82460.18451480.16863637100
2.8246-3.23330.20991470.16433651100
3.2333-4.07320.16541500.1533712100
4.0732-48.5450.20541610.18333956100

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