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- PDB-5n9e: Crystal Structure of Drosophila DHX36 helicase in complex with TG... -

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Basic information

Entry
Database: PDB / ID: 5n9e
TitleCrystal Structure of Drosophila DHX36 helicase in complex with TGGGGATTT
Components
  • CG9323, isoform A
  • DNA (5'-D(P*TP*GP*GP*GP*GP*AP*TP*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 / hydrolase activity / RNA helicase / 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 / hydrolase 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 / 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: 3.007 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: To Be Published
Title: Structural and mechanistic insights into DHX36-mediated innate immunity and G-quadruplex unfolding
Authors: Chen, W.-F. / Rety, S. / Hai-Lei 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 21, 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*TP*GP*GP*GP*GP*AP*TP*TP*T)-3')
D: DNA (5'-D(P*TP*GP*GP*GP*GP*AP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)222,4064
Polymers222,4064
Non-polymers00
Water181
1
A: CG9323, isoform A
C: DNA (5'-D(P*TP*GP*GP*GP*GP*AP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)111,2032
Polymers111,2032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-20 kcal/mol
Surface area38530 Å2
MethodPISA
2
B: CG9323, isoform A
D: DNA (5'-D(P*TP*GP*GP*GP*GP*AP*TP*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 area3160 Å2
ΔGint-22 kcal/mol
Surface area38020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)304.472, 51.242, 164.522
Angle α, β, γ (deg.)90.00, 114.67, 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 / 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*TP*GP*GP*GP*GP*AP*TP*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.: 1 / 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: 3.007→56.62 Å / Num. obs: 44068 / % possible obs: 93.93 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 58.83 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1087 / Net I/σ(I): 10.92
Reflection shellResolution: 3.007→3.114 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.6705 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 4576 / CC1/2: 0.725 / % possible all: 99.85

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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: 3.007→56.62 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.35
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 2149 4.88 %5%
Rwork0.1816 ---
obs0.1853 44035 93.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.007→56.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13643 378 0 1 14022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114305
X-RAY DIFFRACTIONf_angle_d1.31819381
X-RAY DIFFRACTIONf_dihedral_angle_d13.4728804
X-RAY DIFFRACTIONf_chiral_restr0.0672177
X-RAY DIFFRACTIONf_plane_restr0.0092441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0069-3.07690.35751440.26852895X-RAY DIFFRACTION100
3.0769-3.15380.33661470.24262949X-RAY DIFFRACTION100
3.1538-3.23910.32671600.23762918X-RAY DIFFRACTION100
3.2391-3.33440.28641430.22542939X-RAY DIFFRACTION100
3.3344-3.4420.3277780.24851793X-RAY DIFFRACTION93
3.442-3.5650.3268980.23161682X-RAY DIFFRACTION94
3.565-3.70770.36331500.2782858X-RAY DIFFRACTION97
3.7077-3.87650.28421430.20442970X-RAY DIFFRACTION100
3.8765-4.08080.31791530.21672832X-RAY DIFFRACTION97
4.0808-4.33640.2581470.14682985X-RAY DIFFRACTION100
4.3364-4.67120.17511680.12022959X-RAY DIFFRACTION100
4.6712-5.14110.20891530.12252984X-RAY DIFFRACTION100
5.1411-5.88460.22581480.14972976X-RAY DIFFRACTION100
5.8846-7.41250.24641750.16793022X-RAY DIFFRACTION100
7.4125-66.45750.17211420.15093124X-RAY DIFFRACTION99
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)
10.4281-0.0115-0.11480.4332-0.39882.17160.09560.06420.1978-0.03280.1266-0.0097-0.2146-0.467-0.27950.49170.08830.00880.4157-0.05270.4014-60.5673-0.832628.3949
23.8364-0.05340.47161.2381-0.65481.26190.0835-0.7136-0.47270.2288-0.1383-0.15690.3319-0.1280.03950.4808-0.1562-0.04390.69460.07840.321-52.324-26.043669.2409
31.756-0.25830.28771.6892-0.21441.60730.0876-0.436-0.09550.1543-0.0173-0.05410.2009-0.2345-0.08030.3448-0.1102-0.0470.4373-0.00230.2997-51.17-17.582555.2743
41.00380.01890.18310.1581-0.14140.1922-0.0119-0.66340.11670.271-0.1541-0.3835-0.27520.84420.0960.579-0.3408-0.24921.30890.16340.8456-14.9583-13.352860.9022
51.9852-0.06040.03962.08850.16562.8822-0.0358-0.1129-0.5004-0.0486-0.1277-0.10270.28980.85420.12850.3504-0.0168-0.07830.65250.11520.733-19.3062-24.825446.8693
62.5871-1.91770.74371.4531-0.66570.52250.1411-0.1513-0.13940.3315-0.3073-0.3012-0.06450.42680.12690.3647-0.0621-0.10550.60670.15250.6309-29.4389-10.614552.1219
71.2210.33350.73830.8950.60122.9526-0.1184-0.24360.0788-0.11850.0354-0.0762-0.61160.16140.1080.3985-0.067-0.02870.2430.00110.4503-48.37331.313536.9951
81.918-0.5238-0.0661.2932-0.5862.03920.04840.0944-0.2380.0186-0.1201-0.28260.02450.2720.06130.4418-0.0583-0.00830.24360.00350.3657-38.0472-17.132223.1197
92.5459-0.1353-0.80011.2362-0.41592.67560.22580.48350.273-0.2156-0.1308-0.1233-0.4155-0.2515-0.07140.48330.07530.01510.26060.02810.3466-48.47111.002511.8884
101.21930.24560.31640.48170.34362.08510.0996-0.40970.1584-0.0950.01250.0171-0.21560.3716-0.12590.2696-0.05920.04960.40280.01240.3154-93.1568-21.486654.1277
111.9525-0.6325-0.46850.71540.68051.7645-0.0259-0.2727-0.0537-0.12050.01840.184-0.163-0.45360.00620.33640.02430.04610.39720.07040.3591-122.1626-22.86752.6176
121.9879-0.49540.08261.39680.35652.24560.0860.1273-0.0097-0.228-0.06640.0597-0.1234-0.1223-0.00750.4393-0.02010.02560.1890.01430.2435-109.1071-26.530621.9433
133.29110.0588-0.68151.4772-1.051.46110.0203-0.0101-0.3843-0.5699-0.3228-0.331-0.2442-0.11480.24570.41260.0064-0.03820.4497-0.00930.5695-33.0559-16.039237.4596
145.6401-0.50441.58311.80620.28792.25980.04240.1520.1819-0.1228-0.14440.1560.40.1280.17330.5360.00620.02760.41980.05980.3535-115.5871-21.921340.4709
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 314 )
4X-RAY DIFFRACTION4chain 'A' and (resid 315 through 396 )
5X-RAY DIFFRACTION5chain 'A' and (resid 397 through 541 )
6X-RAY DIFFRACTION6chain 'A' and (resid 542 through 584 )
7X-RAY DIFFRACTION7chain 'A' and (resid 585 through 649 )
8X-RAY DIFFRACTION8chain 'A' and (resid 650 through 840 )
9X-RAY DIFFRACTION9chain 'A' and (resid 841 through 929 )
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 314 )
11X-RAY DIFFRACTION11chain 'B' and (resid 315 through 650 )
12X-RAY DIFFRACTION12chain 'B' and (resid 651 through 929 )
13X-RAY DIFFRACTION13chain 'C' and (resid 2 through 10 )
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 10 )

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