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- PDB-5n9d: Crystal Structure of Drosophila DHX36 helicase in complex with GG... -

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Basic information

Entry
Database: PDB / ID: 5n9d
TitleCrystal Structure of Drosophila DHX36 helicase in complex with GGGTTAGGGT
Components
  • CG9323, isoform A
  • DNA (5'-D(P*GP*GP*GP*TP*TP*AP*GP*GP*GP*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: 2.71 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*GP*GP*TP*TP*AP*GP*GP*GP*T)-3')
D: DNA (5'-D(P*GP*GP*GP*TP*TP*AP*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)223,1154
Polymers223,1154
Non-polymers00
Water2,288127
1
A: CG9323, isoform A
C: DNA (5'-D(P*GP*GP*GP*TP*TP*AP*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)111,5572
Polymers111,5572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-16 kcal/mol
Surface area39120 Å2
MethodPISA
2
B: CG9323, isoform A
D: DNA (5'-D(P*GP*GP*GP*TP*TP*AP*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)111,5572
Polymers111,5572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-16 kcal/mol
Surface area39430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)305.436, 51.339, 164.947
Angle α, β, γ (deg.)90.00, 114.80, 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*GP*GP*TP*TP*AP*GP*GP*GP*T)-3')


Mass: 3156.062 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.: 127 / 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 meas: 54.3 Mg/m3 / Density % sol: 53.25 %
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: 2.71→56.68 Å / Num. obs: 63335 / % possible obs: 98.64 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 54.04 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.58
Reflection shellResolution: 2.71→2.807 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5952 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6283 / CC1/2: 0.764 / % possible all: 99.87

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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: 2.71→56.68 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.95
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 3103 4.9 %5%
Rwork0.1852 ---
obs0.1882 63325 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.71→56.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13748 426 0 127 14301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914469
X-RAY DIFFRACTIONf_angle_d1.17319626
X-RAY DIFFRACTIONf_dihedral_angle_d16.4358890
X-RAY DIFFRACTIONf_chiral_restr0.0592206
X-RAY DIFFRACTIONf_plane_restr0.0072468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7098-2.75220.29391320.2452690X-RAY DIFFRACTION100
2.7522-2.79730.32121500.23812736X-RAY DIFFRACTION100
2.7973-2.84550.30171480.24132784X-RAY DIFFRACTION100
2.8455-2.89730.32591240.26482716X-RAY DIFFRACTION100
2.8973-2.9530.33161410.25652714X-RAY DIFFRACTION100
2.953-3.01330.36261500.2492795X-RAY DIFFRACTION100
3.0133-3.07880.27841310.2342712X-RAY DIFFRACTION100
3.0788-3.15040.31141350.21692758X-RAY DIFFRACTION100
3.1504-3.22920.27731500.21772786X-RAY DIFFRACTION100
3.2292-3.31650.31641280.22742717X-RAY DIFFRACTION100
3.3165-3.41410.2921500.22472801X-RAY DIFFRACTION100
3.4141-3.52430.28831360.21272704X-RAY DIFFRACTION100
3.5243-3.65020.30291480.22062766X-RAY DIFFRACTION99
3.6502-3.79640.35291210.23232205X-RAY DIFFRACTION81
3.7964-3.96910.22531350.17362795X-RAY DIFFRACTION99
3.9691-4.17840.21211510.15592740X-RAY DIFFRACTION100
4.1784-4.44010.2021430.14392752X-RAY DIFFRACTION99
4.4401-4.78290.18291420.13222796X-RAY DIFFRACTION99
4.7829-5.2640.20081430.13542775X-RAY DIFFRACTION99
5.264-6.02530.21291560.16712769X-RAY DIFFRACTION99
6.0253-7.58950.19771500.16882830X-RAY DIFFRACTION99
7.5895-66.70320.18641390.15412881X-RAY DIFFRACTION97
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)
10.4576-0.1005-0.09011.1237-0.9373.27110.1153-0.02910.2065-0.08850.10090.1278-0.3135-0.5225-0.24550.35110.021-0.04530.4059-0.06270.3501-60.8604-1.011328.6266
23.13350.09780.20521.7894-0.78152.11240.228-0.7692-0.57560.2543-0.1191-0.08780.4645-0.2531-0.03750.5219-0.1515-0.09480.70780.10690.3639-52.4389-26.129969.4261
31.94390.2622-0.28690.6932-0.47232.27720.0688-0.4941-0.08070.1801-0.1651-0.3093-0.03330.54850.03890.3598-0.1164-0.15350.5080.03360.4376-34.2537-16.776456.7756
42.4725-0.88640.33451.3379-0.30452.75560.04990.0006-0.8803-0.1543-0.1659-0.13910.99430.62020.14510.59040.1313-0.07470.74550.12260.9375-18.5748-32.663644.5493
52.6851-1.29-0.5250.6983-0.07721.5439-0.0188-0.3965-0.16560.2221-0.1371-0.237-0.11930.57720.08290.4126-0.1592-0.14350.59370.10920.5948-26.7685-14.374950.216
61.65030.01020.55891.06070.36313.0790.0144-0.16860.1577-0.0120.0015-0.3417-0.54420.081-0.06780.4442-0.08290.00650.19740.01810.3926-48.56771.084937.0001
72.2579-0.81910.47241.7992-0.96472.66530.00290.1623-0.41120.0538-0.075-0.33550.16760.30330.06250.3351-0.0046-0.00070.2575-0.02360.4786-35.7718-21.616823.6411
81.7184-0.1155-0.10722.1572-0.41092.26330.02690.0547-0.201-0.235-0.1224-0.31670.11950.16810.01640.4081-0.0461-00.20550.01330.3285-40.3002-17.988722.6829
92.0903-0.38680.08451.7701-0.6492.12380.18610.23850.2614-0.116-0.1783-0.4699-0.43120.50140.06070.4871-0.1060.02430.32490.05310.421-34.0402-2.783517.8089
102.2757-0.2695-0.58870.76190.03172.90840.13640.23780.1939-0.4616-0.0649-0.1011-0.2454-0.2661-0.0810.5165-0.0138-0.00070.30320.05390.3361-51.4947-0.176111.7821
110.71860.010.53560.2640.39282.81380.11070.1494-0.1651-0.11330.0821-0.07370.37310.9061-0.22660.34950.00390.01530.5092-0.01910.3697-87.7297-36.42229.9231
122.93330.57230.45910.78690.63561.89590.0529-0.8270.518-0.0023-0.01230.1755-0.59450.2335-0.06360.4939-0.11050.08120.8281-0.17870.4039-94.1625-11.511870.6596
131.7668-0.1103-0.26951.4388-0.03642.45930.1014-0.47640.2519-0.00940.01870.0539-0.33750.3168-0.09090.3165-0.08510.08160.4199-0.03480.2825-95.8076-19.309255.8062
141.8614-1.0632-0.45741.39030.21091.74910.0242-0.5759-0.2087-0.11580.06130.3248-0.1081-0.4893-0.08110.3053-0.0570.08830.58110.10660.3329-123.5911-25.689862.874
152.5651-0.2879-0.69731.70790.66653.05560.0343-0.18760.1057-0.1784-0.04410.1811-0.8197-0.6961-0.15320.48430.21710.01080.6660.060.3752-132.9286-11.83654.29
162.1099-0.9898-0.46250.37490.30061.21130.1196-0.2174-0.3465-0.1329-0.08210.1904-0.132-0.3963-0.03610.3007-0.00560.05160.48090.0950.4007-120.1662-27.896853.3892
171.5002-0.3952-0.54890.81680.14923.78730.0026-0.0695-0.2774-0.1470.08390.10920.6550.1143-0.12180.4023-0.0532-0.00620.19390.01250.3975-100.4183-39.176938.8271
182.4514-0.98810.54911.8891-0.012.0247-0.13150.09550.34860.05780.12890.1284-0.5999-0.140.02760.57680.01230.05070.24980.03720.3557-109.832-13.594728.0199
191.5148-0.3162-0.04251.87410.44072.11190.03250.30220.0413-0.0632-0.0540.3704-0.0544-0.3849-0.04290.5088-0.0383-0.01750.25390.02570.3488-113.9928-28.098621.8565
202.4448-0.714-0.25121.33590.46992.48270.17060.3378-0.2362-0.3412-0.09170.1380.334-0.0058-0.05130.5389-0.0231-0.0040.2417-0.00520.283-107.047-37.031416.5282
219.3524-1.5238-3.40740.42230.49941.2370.00170.54370.0618-0.2556-0.0432-0.1355-0.07-0.2166-0.03290.4759-0.0468-0.12110.62410.04220.6967-36.1937-16.28537.7758
227.6954-0.25651.70720.79880.10920.5789-0.3311.05150.0819-0.30950.1621-0.0272-0.11950.1850.04070.5827-0.00460.11690.48270.03580.3929-113.0901-22.064240.4331
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 418 )
4X-RAY DIFFRACTION4chain 'A' and (resid 419 through 482 )
5X-RAY DIFFRACTION5chain 'A' and (resid 483 through 584 )
6X-RAY DIFFRACTION6chain 'A' and (resid 585 through 649 )
7X-RAY DIFFRACTION7chain 'A' and (resid 650 through 692 )
8X-RAY DIFFRACTION8chain 'A' and (resid 693 through 815 )
9X-RAY DIFFRACTION9chain 'A' and (resid 816 through 864 )
10X-RAY DIFFRACTION10chain 'A' and (resid 865 through 929 )
11X-RAY DIFFRACTION11chain 'B' and (resid 54 through 123 )
12X-RAY DIFFRACTION12chain 'B' and (resid 124 through 196 )
13X-RAY DIFFRACTION13chain 'B' and (resid 197 through 300 )
14X-RAY DIFFRACTION14chain 'B' and (resid 301 through 376 )
15X-RAY DIFFRACTION15chain 'B' and (resid 377 through 508 )
16X-RAY DIFFRACTION16chain 'B' and (resid 509 through 584 )
17X-RAY DIFFRACTION17chain 'B' and (resid 585 through 649 )
18X-RAY DIFFRACTION18chain 'B' and (resid 650 through 743 )
19X-RAY DIFFRACTION19chain 'B' and (resid 744 through 815 )
20X-RAY DIFFRACTION20chain 'B' and (resid 816 through 929 )
21X-RAY DIFFRACTION21chain 'C' and (resid 2 through 11 )
22X-RAY DIFFRACTION22chain 'D' and (resid 2 through 11 )

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