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- PDB-6uv1: Crystal structure of RNA helicase DDX17 in complex of rU10 RNA -

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Basic information

Entry
Database: PDB / ID: 6uv1
TitleCrystal structure of RNA helicase DDX17 in complex of rU10 RNA
Components
  • Probable ATP-dependent RNA helicase DDX17
  • RNA rU10
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: 2.307 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 / 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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
C: RNA rU10
D: RNA rU10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,85418
Polymers108,6254
Non-polymers1,22914
Water9,908550
1
A: Probable ATP-dependent RNA helicase DDX17
C: RNA rU10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,95110
Polymers54,3122
Non-polymers6398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-68 kcal/mol
Surface area19790 Å2
MethodPISA
2
B: Probable ATP-dependent RNA helicase DDX17
D: RNA rU10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9038
Polymers54,3122
Non-polymers5906
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-66 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.752, 91.074, 103.496
Angle α, β, γ (deg.)90.000, 95.560, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 38 through 39 or resid 41...
21(chain B and (resid 42 through 43 or resid 45 through 1002))
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 38 through 39 or resid 41...A38 - 39
121(chain A and (resid 38 through 39 or resid 41...A41 - 42
131(chain A and (resid 38 through 39 or resid 41...A47 - 475
141(chain A and (resid 38 through 39 or resid 41...A1000 - 1002
211(chain B and (resid 42 through 43 or resid 45 through 1002))B42 - 43
221(chain B and (resid 42 through 43 or resid 45 through 1002))B45 - 1002
112chain CC2 - 8
212chain DD2 - 8

NCS ensembles :
ID
1
2

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#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: RNA chain RNA rU10


Mass: 3016.700 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 564 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium citrate pH 6.0, 2M NaCl

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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: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 49393 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.1 Å2 / Rrim(I) all: 0.175 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 2465 / Rrim(I) all: 0.832

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DDX17-rU10

Resolution: 2.307→46.768 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.5
RfactorNum. reflection% reflection
Rfree0.2553 2000 4.05 %
Rwork0.1971 --
obs0.1995 49350 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.4 Å2 / Biso mean: 31.1319 Å2 / Biso min: 10.53 Å2
Refinement stepCycle: final / Resolution: 2.307→46.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6937 264 72 550 7823
Biso mean--20.63 34.02 -
Num. residues----886
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A0X-RAY DIFFRACTION5.881TORSIONAL
12B0X-RAY DIFFRACTION5.881TORSIONAL
21C158X-RAY DIFFRACTION5.881TORSIONAL
22D158X-RAY DIFFRACTION5.881TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.307-2.36450.33291380.2406324496
2.3645-2.42840.3011430.22943403100
2.4284-2.49990.27331420.22453376100
2.4999-2.58060.3211410.22143336100
2.5806-2.67280.28631440.21833403100
2.6728-2.77980.26071430.21123382100
2.7798-2.90630.29081430.21523380100
2.9063-3.05950.30351430.20683382100
3.0595-3.25110.28311420.21313380100
3.2511-3.50210.25241430.19623386100
3.5021-3.85430.25071440.1773408100
3.8543-4.41170.2141430.17453384100
4.4117-5.55680.20541440.16963429100
5.5568-46.7680.22731470.1929345799

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