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- PDB-5n94: Crystal Structure of Drosophila DHX36 helicase in complex with polyU -

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Basic information

Entry
Database: PDB / ID: 5n94
TitleCrystal Structure of Drosophila DHX36 helicase in complex with polyU
Components
  • CG9323, isoform A
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsHYDROLASE / Helicase / DExH / ssDNA
Function / homology
Function and homology information


DEx/H-box helicases activate type I IFN and inflammatory cytokines production / G-quadruplex DNA unwinding / G-quadruplex DNA binding / DNA helicase activity / helicase activity / G-quadruplex RNA binding / RNA helicase activity / RNA helicase / hydrolase activity / ATP binding ...DEx/H-box helicases activate type I IFN and inflammatory cytokines production / G-quadruplex DNA unwinding / G-quadruplex DNA binding / DNA helicase activity / helicase activity / G-quadruplex RNA binding / RNA helicase activity / RNA helicase / hydrolase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase ...: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / 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
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.428 Å
AuthorsChen, W.-F. / Rety, S. / Hai-Lei Guo, H.-L. / Wu, W.-Q. / Liu, N.-N. / Liu, Q.-W. / Dai, Y.-X. / Xi, X.-G.
CitationJournal: Structure / Year: 2018
Title: Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model.
Authors: Chen, W.F. / Rety, S. / Guo, H.L. / Dai, Y.X. / Wu, W.Q. / Liu, N.N. / Auguin, D. / Liu, Q.W. / Hou, X.M. / Dou, S.X. / Xi, X.G.
History
DepositionFeb 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG9323, isoform A
B: CG9323, isoform A
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
D: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)221,6114
Polymers221,6114
Non-polymers00
Water1,20767
1
A: CG9323, isoform A
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)110,8062
Polymers110,8062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-32 kcal/mol
Surface area38200 Å2
MethodPISA
2
B: CG9323, isoform A
D: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)110,8062
Polymers110,8062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-33 kcal/mol
Surface area38170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)338.328, 51.534, 159.899
Angle α, β, γ (deg.)90.00, 118.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CG9323, isoform A / CG9323 / isoform B / GH12763p


Mass: 108401.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG9323, Dmel_CG9323 / Plasmid: pTwin1 / Production host: Escherichia coli (E. coli) / Strain (production host): C2566H / References: UniProt: Q8SWT2, EC: 3.6.1.3
#2: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2404.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES monohydrate-imidazole 20mM sodium formate 20mM ammonium acetate 20mM sodium citrate tribasic hydrate 20mM sodium oxamate 20mM potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9799 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 2.428→47 Å / Num. obs: 84548 / % possible obs: 90.74 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 49.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0468 / Net I/σ(I): 17.44
Reflection shellResolution: 2.428→2.515 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5307 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 9161 / CC1/2: 0.878 / % possible all: 99.41

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N8R

5n8r


Resolution: 2.428→46.997 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.95
RfactorNum. reflection% reflectionSelection details
Rfree0.278 4043 4.78 %5%
Rwork0.2119 ---
obs0.215 84497 90.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.428→46.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13628 320 0 67 14015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114216
X-RAY DIFFRACTIONf_angle_d1.45419242
X-RAY DIFFRACTIONf_dihedral_angle_d16.525552
X-RAY DIFFRACTIONf_chiral_restr0.0562184
X-RAY DIFFRACTIONf_plane_restr0.0072434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4281-2.45670.40651470.33333045X-RAY DIFFRACTION99
2.4567-2.48660.36361540.32423006X-RAY DIFFRACTION99
2.4866-2.51810.36321540.30382984X-RAY DIFFRACTION99
2.5181-2.55130.39121300.31353035X-RAY DIFFRACTION99
2.5513-2.58620.3851600.30413048X-RAY DIFFRACTION100
2.5862-2.62310.38341600.28892958X-RAY DIFFRACTION99
2.6231-2.66230.3419460.30711025X-RAY DIFFRACTION88
2.7039-2.74820.32611190.27592445X-RAY DIFFRACTION95
2.7482-2.79560.33081460.28063010X-RAY DIFFRACTION99
2.7956-2.84640.36891580.27933053X-RAY DIFFRACTION100
2.8464-2.90120.37541300.27783038X-RAY DIFFRACTION100
2.9012-2.96040.34981540.27422995X-RAY DIFFRACTION100
2.9604-3.02470.37181830.26323010X-RAY DIFFRACTION99
3.0247-3.09510.28871550.25232977X-RAY DIFFRACTION99
3.0951-3.17250.32941460.25273082X-RAY DIFFRACTION100
3.1725-3.25820.30861760.2472999X-RAY DIFFRACTION99
3.2582-3.35410.34391590.24512978X-RAY DIFFRACTION100
3.3541-3.46230.28561360.24882960X-RAY DIFFRACTION96
3.4623-3.5860.31491370.24343036X-RAY DIFFRACTION99
3.586-3.72950.3031030.23771343X-RAY DIFFRACTION44
3.7295-3.89920.27261540.20982929X-RAY DIFFRACTION97
3.8992-4.10470.2821750.20032943X-RAY DIFFRACTION97
4.1047-4.36170.25341550.18073049X-RAY DIFFRACTION99
4.3617-4.69810.21461260.16083079X-RAY DIFFRACTION99
4.6981-5.17040.20321350.16333080X-RAY DIFFRACTION99
5.1704-5.91730.24571700.18133009X-RAY DIFFRACTION98
5.9173-7.45040.24651530.17973119X-RAY DIFFRACTION99
7.4504-47.00570.15391220.14043219X-RAY DIFFRACTION98

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