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- PDB-6uv0: Crystal structure of apo core domain of RNA helicase DDX17 -

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Basic information

Entry
Database: PDB / ID: 6uv0
TitleCrystal structure of apo core domain of RNA helicase DDX17
ComponentsProbable ATP-dependent RNA helicase DDX17
KeywordsRNA BINDING PROTEIN / DEAD-box ATPase / RNA helicase / RNA binding
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
Probable ATP-dependent RNA helicase DDX17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 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 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 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
B: Probable ATP-dependent RNA helicase DDX17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6163
Polymers102,5912
Non-polymers241
Water1,76598
1
A: Probable ATP-dependent RNA helicase DDX17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3202
Polymers51,2961
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable ATP-dependent RNA helicase DDX17


Theoretical massNumber of molelcules
Total (without water)51,2961
Polymers51,2961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.649, 97.811, 154.924
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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.: 2
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 24% PEG, 0.26M NaSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.07218 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07218 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 32184 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rrim(I) all: 0.152 / Net I/σ(I): 42.8
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 1564 / Rrim(I) all: 0.824

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo DDX17

Resolution: 2.601→48.906 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.8
RfactorNum. reflection% reflection
Rfree0.2595 1998 6.22 %
Rwork0.213 --
obs0.216 32109 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 186.54 Å2 / Biso mean: 70 Å2 / Biso min: 19.98 Å2
Refinement stepCycle: final / Resolution: 2.601→48.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6662 0 1 98 6761
Biso mean--30.29 47.89 -
Num. residues----829
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6013-2.66630.35351330.2906200194
2.6663-2.73840.3741390.27209098
2.7384-2.8190.26971440.25682159100
2.819-2.90990.29551390.24472105100
2.9099-3.01390.28981400.25332109100
3.0139-3.13460.27661430.2432166100
3.1346-3.27720.3131420.24622136100
3.2772-3.450.28651440.22442153100
3.45-3.6660.28361420.20362143100
3.666-3.9490.25521440.19892171100
3.949-4.34620.22231430.18712166100
4.3462-4.97450.20971460.16412191100
4.9745-6.26530.23041470.2182224100
6.2653-48.9060.241520.2026229799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.64670.2471-0.10793.9573-0.8971.85-0.0694-0.01450.1233-0.0407-0.0009-0.13230.01480.0270.07370.19190.0073-0.01760.2545-0.05920.2313.7778-26.8021-16.8873
25.5327-0.749-3.56722.78050.02532.37780.17710.67780.6942-0.07970.4080.6257-0.3248-0.9191-0.54470.39590.0494-0.08660.4970.04680.7207-1.7147-16.5551-16.6358
33.47894.7991-1.34237.0684-1.7043.2887-0.0612-0.18880.0867-0.2604-0.1154-0.0882-0.46220.01630.12880.6450.034-0.14320.43790.00850.8827-20.6243-1.2194-22.6796
41.48450.64930.11455.4297-1.43232.15380.08930.0721-0.2925-0.1595-0.1432-0.23870.28010.15140.06370.2940.05770.0310.31950.00830.262619.7587-3.4654-57.3428
51.99770.1031-0.15914.2619-4.38445.8855-0.46560.53931.08780.03270.28920.8444-0.5049-0.31880.19311.052-0.1478-0.2470.73060.20421.4241-15.6672-28.1357-56.9669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 281 )A40 - 281
2X-RAY DIFFRACTION2chain 'A' and (resid 282 through 313 )A282 - 313
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 475 )A314 - 475
4X-RAY DIFFRACTION4chain 'B' and (resid 42 through 310 )B42 - 310
5X-RAY DIFFRACTION5chain 'B' and (resid 311 through 468 )B311 - 468

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