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- PDB-5n9f: Crystal Structure of Drosophila DHX36 helicase in complex with ss... -

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Basic information

Entry
Database: PDB / ID: 5n9f
TitleCrystal Structure of Drosophila DHX36 helicase in complex with ssDNA CpG_A
Components
  • CG9323, isoform A
  • DNA (5'-D(*GP*GP*GP*GP*AP*CP*GP*AP*TP*C)-3')
KeywordsHYDROLASE / Helicase / DExH / ssDNA
Function / homology
Function and homology information


DEx/H-box helicases activate type I IFN and inflammatory cytokines production / DNA geometric change / G-quadruplex DNA binding / DNA 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 (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 / MOLECULAR REPLACEMENT / Resolution: 2.969 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

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Assembly

Deposited unit
A: CG9323, isoform A
B: CG9323, isoform A
C: DNA (5'-D(*GP*GP*GP*GP*AP*CP*GP*AP*TP*C)-3')
D: DNA (5'-D(*GP*GP*GP*GP*AP*CP*GP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,0816
Polymers223,0234
Non-polymers582
Water00
1
A: CG9323, isoform A
C: DNA (5'-D(*GP*GP*GP*GP*AP*CP*GP*AP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)111,5112
Polymers111,5112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-12 kcal/mol
Surface area38740 Å2
MethodPISA
2
B: CG9323, isoform A
D: DNA (5'-D(*GP*GP*GP*GP*AP*CP*GP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5704
Polymers111,5112
Non-polymers582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-40 kcal/mol
Surface area38830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)306.683, 51.311, 164.860
Angle α, β, γ (deg.)90.00, 115.55, 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(*GP*GP*GP*GP*AP*CP*GP*AP*TP*C)-3')


Mass: 3110.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: part of ssDNA CpG_A / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 2.969→67.1 Å / Num. obs: 46639 / % possible obs: 95.36 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 68.15 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.135 / Net I/σ(I): 6.7
Reflection shellResolution: 2.969→3.075 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5152 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 4799 / CC1/2: 0.942 / % possible all: 99.23

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Processing

Software
NameVersionClassification
PHENIX(1.11_2563: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N8R

5n8r


Resolution: 2.969→67.1 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.7
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 2300 4.93 %5%
Rwork0.2142 ---
obs0.2169 46636 95.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.969→67.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13744 387 2 0 14133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414421
X-RAY DIFFRACTIONf_angle_d0.68119544
X-RAY DIFFRACTIONf_dihedral_angle_d5.3488876
X-RAY DIFFRACTIONf_chiral_restr0.0442195
X-RAY DIFFRACTIONf_plane_restr0.0042460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9688-3.03340.40761560.33722881X-RAY DIFFRACTION99
3.0334-3.10390.36361420.29162808X-RAY DIFFRACTION99
3.1039-3.18150.32841520.28172917X-RAY DIFFRACTION99
3.1815-3.26760.3321650.27972776X-RAY DIFFRACTION99
3.2676-3.36370.39311390.2962861X-RAY DIFFRACTION99
3.3637-3.47230.331120.26422289X-RAY DIFFRACTION80
3.4723-3.59640.32981570.25362864X-RAY DIFFRACTION99
3.5964-3.74040.29491100.2342183X-RAY DIFFRACTION76
3.7404-3.91060.27441180.22082301X-RAY DIFFRACTION80
3.9106-4.11670.28461560.20992835X-RAY DIFFRACTION99
4.1167-4.37460.24131650.18382874X-RAY DIFFRACTION100
4.3746-4.71230.22351400.17482922X-RAY DIFFRACTION100
4.7123-5.18640.23741460.1692920X-RAY DIFFRACTION100
5.1864-5.93650.26931360.20332924X-RAY DIFFRACTION100
5.9365-7.4780.22681640.20892945X-RAY DIFFRACTION99
7.478-69.19120.20921420.18043036X-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)
11.38340.37120.32120.81780.43382.59690.128-0.56610.1404-0.00540.00750.0297-0.35540.4618-0.1390.3838-0.09180.08610.5850.00320.407958.026916.541253.7967
20.3754-0.3273-0.63761.1498-0.09291.801-0.1718-0.4355-0.34620.02010.27680.7365-0.4551-0.318-0.11060.50670.05390.22360.82360.07430.808117.101214.254964.3991
32.1579-1.0639-0.82440.93880.60212.28410.0007-0.285-0.13780.02010.05270.3179-0.4163-0.375-0.08890.46010.00430.04320.44360.06850.482332.422816.461148.2464
42.4816-0.7617-0.33852.82330.66362.8320.11940.1735-0.0352-0.2217-0.10210.2967-0.1417-0.1738-0.02940.5294-0.05120.00470.26870.04810.291442.373212.40821.5247
50.9573-0.0518-0.37250.9702-1.17744.81250.2702-0.03340.206-0.05140.13870.127-0.6743-0.7642-0.41890.50260.02360.03850.4553-0.04180.4858-61.314212.335328.5275
63.20270.02430.03231.3956-0.25572.24140.0825-0.7618-0.15640.2347-0.0561-0.45550.12250.1825-0.04190.4772-0.087-0.2150.57710.03990.5805-39.8494-5.783959.8836
72.6358-1.33680.98861.5351-0.90582.46220.0413-0.07270.05170.0217-0.1027-0.51160.04970.51870.0650.3879-0.0772-0.0540.4082-0.01350.6443-31.1653-1.603745.3727
82.0448-0.2026-0.01232.6125-0.71382.82150.01740.1576-0.0628-0.1758-0.096-0.4097-0.00270.08950.07990.4787-0.03480.05350.2937-0.05470.3524-41.46931.843419.6198
99.3461-2.43011.68274.0443-0.73477.0238-0.19330.42670.1253-0.0693-0.3123-0.56430.00271.46450.37160.9012-0.02910.26790.87020.01820.646737.478317.155640.5713
103.0908-1.31511.48751.99230.74612.00410.30490.0813-0.1205-0.1102-0.23940.359-0.3996-1.6282-0.05120.79350.0938-0.12311.14460.00251.3607-34.6568-2.70237.7734
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 396 )
3X-RAY DIFFRACTION3chain 'A' and (resid 397 through 650 )
4X-RAY DIFFRACTION4chain 'A' and (resid 651 through 929 )
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 123 )
6X-RAY DIFFRACTION6chain 'B' and (resid 124 through 418 )
7X-RAY DIFFRACTION7chain 'B' and (resid 419 through 649 )
8X-RAY DIFFRACTION8chain 'B' and (resid 650 through 929 )
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 11 )
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 11 )

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