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- PDB-5n8r: Crystal Structure of Drosophilia DHX36 helicase in complex with G... -

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Basic information

Entry
Database: PDB / ID: 5n8r
TitleCrystal Structure of Drosophilia DHX36 helicase in complex with GAGCACTGC
Components
  • CG9323, isoform A
  • DNA (5'-D(P*GP*AP*GP*CP*AP*CP*TP*GP*C)-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 binding / DNA helicase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / helicase activity / G-quadruplex RNA binding ...DEx/H-box helicases activate type I IFN and inflammatory cytokines production / : / G-quadruplex DNA binding / DNA helicase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / helicase activity / G-quadruplex RNA binding / hydrolase activity / RNA helicase activity / RNA helicase / 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 (HA2), winged-helix / Helicase-associated domain / 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 domain ...: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / 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 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
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 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.
Funding support China, France, 3items
OrganizationGrant numberCountry
Natural Science Foundation31370798, 11574252 China
CNRS/ International Associated LaboratoryLIA "G quadruplex-HELI" France
CNRS/ International Associated LaboratoryLIA "G quadruplex-HELI" China
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 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: DNA (5'-D(P*GP*AP*GP*CP*AP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*GP*AP*GP*CP*AP*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)222,2844
Polymers222,2844
Non-polymers00
Water15,006833
1
A: CG9323, isoform A
C: DNA (5'-D(P*GP*AP*GP*CP*AP*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)111,1422
Polymers111,1422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-11 kcal/mol
Surface area38210 Å2
MethodPISA
2
B: CG9323, isoform A
D: DNA (5'-D(P*GP*AP*GP*CP*AP*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)111,1422
Polymers111,1422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-10 kcal/mol
Surface area37830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)300.866, 51.477, 164.393
Angle α, β, γ (deg.)90.00, 114.22, 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: DNA chain DNA (5'-D(P*GP*AP*GP*CP*AP*CP*TP*GP*C)-3')


Mass: 2740.812 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: single-stranded DNA / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 833 / 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: BL17U / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→149.9 Å / Num. obs: 117031 / % possible obs: 99.26 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 35.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07341 / Net I/σ(I): 13.08
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6078 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 11661 / CC1/2: 0.738 / % possible all: 99.52

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→149.9 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.76
RfactorNum. reflection% reflection
Rfree0.2186 5865 5.01 %
Rwork0.1761 --
obs0.1782 117070 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→149.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13643 370 0 833 14846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914297
X-RAY DIFFRACTIONf_angle_d1.14919365
X-RAY DIFFRACTIONf_dihedral_angle_d14.478804
X-RAY DIFFRACTIONf_chiral_restr0.0652177
X-RAY DIFFRACTIONf_plane_restr0.0082441
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)
10.7049-0.013-0.20450.5518-0.33442.00820.019-0.2423-0.01650.01510.0416-0.00260.0653-0.1727-0.06570.2224-0.0178-0.01720.3022-0.04640.276798.19710.535552.7376
21.7384-0.20540.4230.2029-0.25230.76170.03-0.1083-0.149-0.0396-0.0127-0.1179-0.00880.2206-0.01510.2483-0.0044-0.02490.2842-0.03960.3619126.70599.821248.3889
30.8893-0.1565-0.13651.2344-0.07441.48240.05540.0855-0.0084-0.152-0.0241-0.1349-0.12180.0803-0.03810.3452-0.01750.00030.2228-0.02690.2368110.673614.288419.2649
40.3093-0.0930.3940.44830.49291.91450.17060.1819-0.18-0.14420.0677-0.08570.40250.723-0.16370.40430.0873-0.01310.4999-0.01980.324963.4487-10.134129.9035
52.49540.598-0.54970.60630.41680.7130.0709-0.37060.3913-0.08610.02070.1114-0.2126-0.0048-0.07620.3218-0.03430.01750.5391-0.05080.281960.202118.456571.5678
61.06250.2065-0.03330.98590.25821.49150.0141-0.2810.0633-0.0808-0.00590.0171-0.16280.2049-0.00110.2239-0.03810.03790.2986-0.01380.238755.57977.728258.068
71.1792-0.33470.00980.8708-0.01480.9527-0.0172-0.27580.0054-0.09660.01950.2296-0.049-0.3101-0.01060.2320.00920.00940.39330.02160.301821.34737.625460.2527
81.6147-1.0011-0.10220.65370.3330.7480.0481-0.14760.0661-0.17140.0095-0.0779-0.0647-0.1317-0.03190.2437-0.00010.03080.30170.02610.303430.80375.86352.8368
91.1921-0.33340.41220.8626-0.48931.96430.07270.04350.0314-0.1424-0.01350.0527-0.1972-0.0546-0.05180.3532-0.0110.0430.15120.00430.240546.41543.009731.2399
101.3646-0.2709-0.45051.48780.37971.39170.15020.1802-0.251-0.1317-0.10240.30510.2642-0.2981-0.0390.4513-0.0348-0.0550.2575-0.00860.28432.3188-7.25422.2071
111.98220.1230.50670.89210.25982.05920.18640.3271-0.1836-0.3115-0.00170.02820.29230.2557-0.16430.56210.078-0.01830.272-0.04030.263950.651-12.063813.5102
122.91690.3429-0.80380.4831-0.39230.9413-0.14240.5485-0.3465-0.05210.0084-0.24690.0116-0.12620.10460.3103-0.0273-0.0540.3558-0.06560.3952118.6869.395537.0591
136.0442-0.04650.83330.15380.01820.7989-0.14510.3431-0.2188-0.2390.00750.13180.1077-0.04540.0870.4062-0.00450.05920.28760.02140.395635.54394.338940.5388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 321 )
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 649 )
3X-RAY DIFFRACTION3chain 'A' and (resid 650 through 929 )
4X-RAY DIFFRACTION4chain 'B' and (resid 54 through 123 )
5X-RAY DIFFRACTION5chain 'B' and (resid 124 through 168 )
6X-RAY DIFFRACTION6chain 'B' and (resid 169 through 300 )
7X-RAY DIFFRACTION7chain 'B' and (resid 301 through 462 )
8X-RAY DIFFRACTION8chain 'B' and (resid 463 through 584 )
9X-RAY DIFFRACTION9chain 'B' and (resid 585 through 763 )
10X-RAY DIFFRACTION10chain 'B' and (resid 764 through 863 )
11X-RAY DIFFRACTION11chain 'B' and (resid 864 through 929 )
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 10 )
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 10 )

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