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- PDB-5n9a: Crystal Structure of Drosophila DHX36 helicase in complex with GT... -

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Basic information

Entry
Database: PDB / ID: 5n9a
TitleCrystal Structure of Drosophila DHX36 helicase in complex with GTTAGGGTT
Components
  • CG9323, isoform A
  • DNA (5'-D(P*GP*TP*TP*AP*GP*GP*GP*TP*T)-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: 3.036 Å
AuthorsChen, W.-F. / Rety, S. / 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: DNA (5'-D(P*GP*TP*TP*AP*GP*GP*GP*TP*T)-3')
D: DNA (5'-D(P*GP*TP*TP*AP*GP*GP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)222,4064
Polymers222,4064
Non-polymers00
Water543
1
A: CG9323, isoform A
C: DNA (5'-D(P*GP*TP*TP*AP*GP*GP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)111,2032
Polymers111,2032
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-17 kcal/mol
Surface area38870 Å2
MethodPISA
2
B: CG9323, isoform A
D: DNA (5'-D(P*GP*TP*TP*AP*GP*GP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)111,2032
Polymers111,2032
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-18 kcal/mol
Surface area38660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)305.566, 51.424, 165.361
Angle α, β, γ (deg.)90.00, 114.94, 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) / Variant (production host): C2566H / References: UniProt: Q8SWT2, EC: 3.6.1.3
#2: DNA chain DNA (5'-D(P*GP*TP*TP*AP*GP*GP*GP*TP*T)-3')


Mass: 2801.844 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.: 3 / 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: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.036→69.27 Å / Num. obs: 44188 / % possible obs: 96.04 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 62.33 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.1171 / Net I/σ(I): 9.18
Reflection shellResolution: 3.036→3.145 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5895 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 4476 / CC1/2: 0.731 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX(dev_2427: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N8R

5n8r


Resolution: 3.036→69.27 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.22
RfactorNum. reflection% reflectionSelection details
Rfree0.2972 2170 4.91 %5%
Rwork0.2155 ---
obs0.2196 44205 96.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.036→69.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13662 347 0 3 14012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114288
X-RAY DIFFRACTIONf_angle_d1.29419352
X-RAY DIFFRACTIONf_dihedral_angle_d13.7078801
X-RAY DIFFRACTIONf_chiral_restr0.0682174
X-RAY DIFFRACTIONf_plane_restr0.0092442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0355-3.10620.39381620.31162819X-RAY DIFFRACTION100
3.1062-3.18380.431500.28332886X-RAY DIFFRACTION100
3.1838-3.26990.32831600.27412856X-RAY DIFFRACTION100
3.2699-3.36610.40531450.25862894X-RAY DIFFRACTION100
3.3661-3.47480.36011140.24152164X-RAY DIFFRACTION75
3.4748-3.5990.32341430.22612884X-RAY DIFFRACTION100
3.599-3.74310.30941360.22222489X-RAY DIFFRACTION87
3.7431-3.91340.35451160.20942510X-RAY DIFFRACTION97
3.9134-4.11980.29971490.21082823X-RAY DIFFRACTION98
4.1198-4.37790.24521360.18612928X-RAY DIFFRACTION100
4.3779-4.71580.26711510.17822919X-RAY DIFFRACTION100
4.7158-5.19040.23571200.17352952X-RAY DIFFRACTION100
5.1904-5.94120.26591620.19312909X-RAY DIFFRACTION100
5.9412-7.48450.27741630.23212971X-RAY DIFFRACTION100
7.4845-82.00090.26711630.21753031X-RAY DIFFRACTION98
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)
11.03530.7545-0.88780.5852-1.26564.00570.0122-0.03310.4193-0.20670.29340.15910.0729-0.2589-0.33860.45830.05380.08970.3715-0.01950.4995-60.8032-0.5128.503
24.5320.50650.20891.9161-0.74332.62630.0597-0.9035-0.2874-0.1658-0.0727-0.02690.18960.0028-0.00620.4456-0.1669-0.05410.68530.08140.3398-52.8464-25.759669.3949
31.1520.1822-0.86370.7107-0.12321.46530.1502-0.4672-0.17060.1468-0.2285-0.4603-0.07020.52690.0180.3657-0.12-0.15620.68810.10930.5937-29.7484-18.359653.1139
41.58820.0278-0.20871.1858-0.01332.51390.10710.11740.0165-0.1325-0.1762-0.1785-0.10360.1280.07330.3553-0.0239-0.01680.25770.06020.4089-42.8034-8.692522.891
51.23030.08870.36290.63810.58022.22270.0656-0.44740.1589-0.05120.05850.0176-0.18470.3538-0.12950.3315-0.07210.07360.4608-0.0060.3705-93.8125-21.002753.2355
62.085-0.8746-0.36140.96610.34251.78290.0615-0.4152-0.1308-0.07380.05450.255-0.253-0.4404-0.08780.378-0.05590.06160.47530.03460.4514-122.139-22.713553.4064
71.6549-0.4065-0.06521.18750.37242.10360.14210.1664-0.0081-0.1538-0.12390.0422-0.1909-0.1535-0.00950.5412-0.02160.02890.22810.0260.3105-109.7849-26.201321.9641
86.7402-3.55481.72685.48781.44491.9844-0.0984-0.03890.0559-0.4430.03620.4195-0.8369-1.10780.01280.4820.0169-0.11490.78470.21531.0706-31.6408-15.799837.3858
94.9789-2.7355-3.82246.2585-0.30664.16920.27790.3494-0.2905-1.4543-0.1566-0.60430.98540.6005-0.21760.94240.09090.18910.5532-0.1090.7565-118.1277-21.644540.2951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 123 )
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 196 )
3X-RAY DIFFRACTION3chain 'A' and (resid 197 through 584 )
4X-RAY DIFFRACTION4chain 'A' and (resid 585 through 929 )
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 300 )
6X-RAY DIFFRACTION6chain 'B' and (resid 301 through 649 )
7X-RAY DIFFRACTION7chain 'B' and (resid 650 through 929 )
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 10 )
9X-RAY DIFFRACTION9chain 'D' and (resid 2 through 10 )

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