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- PDB-5n90: Crystal Structure of Drosophila DHX36 helicase in complex with TT... -

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Basic information

Entry
Database: PDB / ID: 5n90
TitleCrystal Structure of Drosophila DHX36 helicase in complex with TTGTGGTGT
Components
  • CG9323, isoform A
  • DNA (5'-D(P*TP*TP*GP*TP*GP*GP*TP*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 / 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
PHOSPHATE ION / DNA / RNA helicase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.069 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

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Assembly

Deposited unit
A: CG9323, isoform A
B: CG9323, isoform A
C: DNA (5'-D(P*TP*TP*GP*TP*GP*GP*TP*GP*T)-3')
D: DNA (5'-D(P*TP*TP*GP*TP*GP*GP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,5786
Polymers222,3884
Non-polymers1902
Water00
1
A: CG9323, isoform A
C: DNA (5'-D(P*TP*TP*GP*TP*GP*GP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2893
Polymers111,1942
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-29 kcal/mol
Surface area38580 Å2
MethodPISA
2
B: CG9323, isoform A
D: DNA (5'-D(P*TP*TP*GP*TP*GP*GP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2893
Polymers111,1942
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-29 kcal/mol
Surface area38620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)307.025, 50.993, 165.266
Angle α, β, γ (deg.)90.00, 115.38, 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(P*TP*TP*GP*TP*GP*GP*TP*GP*T)-3')


Mass: 2792.830 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.069→74.66 Å / Num. obs: 44213 / % possible obs: 99.86 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 73.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1175 / Net I/σ(I): 14.28
Reflection shellResolution: 3.069→3.179 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.8327 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 4405 / CC1/2: 0.76 / % possible all: 99.93

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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: 3.069→74.66 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 2193 4.96 %5%
Rwork0.1864 ---
obs0.1889 44200 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.069→74.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13628 376 10 0 14014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114292
X-RAY DIFFRACTIONf_angle_d1.25519362
X-RAY DIFFRACTIONf_dihedral_angle_d12.0868792
X-RAY DIFFRACTIONf_chiral_restr0.0692176
X-RAY DIFFRACTIONf_plane_restr0.0082436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0692-3.1360.3151280.25672598X-RAY DIFFRACTION100
3.136-3.20890.34321200.28962617X-RAY DIFFRACTION100
3.2089-3.28920.38471330.28962570X-RAY DIFFRACTION100
3.2892-3.37810.31991450.2632643X-RAY DIFFRACTION100
3.3781-3.47750.30241260.23272565X-RAY DIFFRACTION100
3.4775-3.58970.28121370.22642609X-RAY DIFFRACTION100
3.5897-3.7180.28241330.21282607X-RAY DIFFRACTION100
3.718-3.86690.25391330.20892603X-RAY DIFFRACTION100
3.8669-4.04290.23291260.20142615X-RAY DIFFRACTION100
4.0429-4.2560.21661410.16842648X-RAY DIFFRACTION100
4.256-4.52270.20981330.14992610X-RAY DIFFRACTION100
4.5227-4.87180.19251450.14672600X-RAY DIFFRACTION100
4.8718-5.36210.2231330.15392656X-RAY DIFFRACTION100
5.3621-6.13780.2181540.17082624X-RAY DIFFRACTION100
6.1378-7.73210.2081640.17712668X-RAY DIFFRACTION100
7.7321-85.08490.19241420.15442774X-RAY DIFFRACTION99

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