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- PDB-5n8u: Crystal Structure of Drosophila DHX36 helicase in complex with CTCTCCT -

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Basic information

Entry
Database: PDB / ID: 5n8u
TitleCrystal Structure of Drosophila DHX36 helicase in complex with CTCTCCT
Components
  • CG9323, isoform A
  • DNA (5'-D(P*CP*TP*CP*TP*CP*CP*CP*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
PHOSPHATE ION / DNA / RNA helicase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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: To Be Published
Title: Structural and mechanistic insights into DHX36-mediated innate immunity and G-quadruplex unfolding
Authors: Chen, W.-F. / Rety, S. / Guo, H.-L. / Wu, W.-Q. / Liu, N.-N. / Liu, Q.-W. / Dai, Y.-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*CP*TP*CP*TP*CP*CP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*CP*TP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,6206
Polymers221,4304
Non-polymers1902
Water2,918162
1
A: CG9323, isoform A
C: DNA (5'-D(P*CP*TP*CP*TP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8103
Polymers110,7152
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-25 kcal/mol
Surface area38190 Å2
MethodPISA
2
B: CG9323, isoform A
D: DNA (5'-D(P*CP*TP*CP*TP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8103
Polymers110,7152
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-25 kcal/mol
Surface area37900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)302.368, 51.288, 164.097
Angle α, β, γ (deg.)90.00, 114.70, 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*CP*TP*CP*TP*CP*CP*CP*T)-3')


Mass: 2313.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: BL17B1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.62→56.38 Å / Num. obs: 68808 / % possible obs: 98.32 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.52
Reflection shellResolution: 2.62→2.714 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 6930 / CC1/2: 0.8 / % possible all: 99.78

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N8R

5n8r


Resolution: 2.62→56.3 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.87
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 3434 4.99 %5%
Rwork0.1825 ---
obs0.1859 68771 98.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57.46 Å2
Refinement stepCycle: LAST / Resolution: 2.62→56.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13628 310 10 162 14110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114214
X-RAY DIFFRACTIONf_angle_d1.37719234
X-RAY DIFFRACTIONf_dihedral_angle_d14.8978772
X-RAY DIFFRACTIONf_chiral_restr0.072168
X-RAY DIFFRACTIONf_plane_restr0.0092434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6197-2.65560.35031390.27362655X-RAY DIFFRACTION100
2.6556-2.69350.40951180.25882679X-RAY DIFFRACTION100
2.6935-2.73370.33341380.24842595X-RAY DIFFRACTION100
2.7337-2.77650.33731270.2492598X-RAY DIFFRACTION100
2.7765-2.8220.3761530.25812562X-RAY DIFFRACTION98
2.822-2.87060.35541360.24422654X-RAY DIFFRACTION100
2.8706-2.92280.29471440.23782584X-RAY DIFFRACTION100
2.9228-2.97910.31411390.23922630X-RAY DIFFRACTION100
2.9791-3.03990.36021460.24292631X-RAY DIFFRACTION100
3.0399-3.10590.30061360.22822586X-RAY DIFFRACTION99
3.1059-3.17820.31291380.22752673X-RAY DIFFRACTION100
3.1782-3.25770.33871200.23722468X-RAY DIFFRACTION94
3.2577-3.34570.32891370.22312591X-RAY DIFFRACTION99
3.3457-3.44420.24981300.20372659X-RAY DIFFRACTION99
3.4442-3.55530.27311330.19672581X-RAY DIFFRACTION99
3.5553-3.68240.25651580.17982637X-RAY DIFFRACTION99
3.6824-3.82980.26441420.17232583X-RAY DIFFRACTION99
3.8298-4.0040.2431280.16442638X-RAY DIFFRACTION98
4.004-4.21510.19981240.14892645X-RAY DIFFRACTION99
4.2151-4.47910.20171350.14112591X-RAY DIFFRACTION98
4.4791-4.82470.17681370.13652623X-RAY DIFFRACTION98
4.8247-5.30990.2261510.14582622X-RAY DIFFRACTION98
5.3099-6.07750.20811540.17352646X-RAY DIFFRACTION99
6.0775-7.6540.19611310.17312687X-RAY DIFFRACTION98
7.654-56.39360.21981400.15832519X-RAY DIFFRACTION89
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)
10.63240.0959-0.1660.549-0.20421.88070.0348-0.01480.063-0.0661-0.04350.0447-0.0727-0.43720.01030.43620.04630.01490.504-0.01660.5329-60.7899-3.425334.8676
22.2101-0.00340.33071.2703-0.24671.7720.1915-0.5333-0.27560.1057-0.01-0.09720.4456-0.2859-0.15660.4572-0.1299-0.06140.5370.03170.3752-50.6313-21.884360.7379
32.6426-0.2090.15530.1215-0.08790.94550.154-0.2029-0.19870.016-0.1619-0.17980.0470.24580.02730.4204-0.0282-0.10490.45960.01880.6144-23.7723-15.568652.6876
41.0078-0.1789-0.09941.16790.09861.49930.04190.14210.0264-0.1314-0.064-0.2387-0.12460.0680.02160.4286-0.00030.00810.2870.02840.3969-41.5726-6.626222.7165
51.38810.08510.18690.65420.51911.73370.0539-0.470.1161-0.09210.02820.0027-0.1960.3828-0.07490.3585-0.05170.04360.5284-0.00030.3684-93.4969-18.965153.7565
61.9906-0.8658-0.1390.82170.40591.3425-0.0921-0.3177-0.0063-0.08980.10360.1573-0.0842-0.3280.01310.3701-0.01140.0210.53010.05110.4243-127.8147-15.308556.1158
71.3871-0.34090.40460.8589-0.12881.48650.08450.1422-0.0973-0.19650.00550.0726-0.021-0.0229-0.07850.4814-0.07950.01280.25650.0040.331-107.4619-26.056125.2147
80.74280.06360.71471.30560.42050.77820.26050.5390.1135-0.3016-0.03950.5386-0.1906-1.1524-0.31450.78160.0895-0.10370.92770.13351.0017-29.8142-14.158236.7094
92.6983-0.7499-1.48631.7659-0.1541.09430.3180.5492-0.2548-0.6248-0.0551-0.53290.20350.8968-0.22620.7667-0.00890.07710.67510.08080.7399-118.2311-18.807440.0397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 136 )
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 264 )
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 584 )
4X-RAY DIFFRACTION4chain 'A' and (resid 585 through 929 )
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 321 )
6X-RAY DIFFRACTION6chain 'B' and (resid 322 through 584 )
7X-RAY DIFFRACTION7chain 'B' and (resid 585 through 929 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 8 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 8 )

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