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- PDB-5n8z: Crystal Structure of Drosophila DHX36 helicase in complex with CT... -

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Basic information

Entry
Database: PDB / ID: 5n8z
TitleCrystal Structure of Drosophila DHX36 helicase in complex with CTCTCCCTT
Components
  • CG9323, isoform A
  • DNA (5'-D(P*CP*TP*CP*TP*CP*CP*CP*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 / 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: 3.477 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

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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*TP*T)-3')
D: DNA (5'-D(P*CP*TP*CP*TP*CP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,2286
Polymers222,0384
Non-polymers1902
Water00
1
A: CG9323, isoform A
C: DNA (5'-D(P*CP*TP*CP*TP*CP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1143
Polymers111,0192
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-31 kcal/mol
Surface area38690 Å2
MethodPISA
2
B: CG9323, isoform A
D: DNA (5'-D(P*CP*TP*CP*TP*CP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1143
Polymers111,0192
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-29 kcal/mol
Surface area38570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)306.251, 51.171, 165.177
Angle α, β, γ (deg.)90.00, 115.30, 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*CP*TP*CP*TP*CP*CP*CP*TP*T)-3')


Mass: 2617.723 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: BL17U / 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: 3.47→40.98 Å / Num. obs: 29426 / % possible obs: 95.87 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.169 / Net I/σ(I): 9.06
Reflection shellResolution: 3.477→3.601 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 3035 / CC1/2: 0.66 / % possible all: 99.67

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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: 3.477→40 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 1459 4.96 %5%
Rwork0.1975 ---
obs0.2011 29402 95.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.477→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13628 350 10 0 13988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01214258
X-RAY DIFFRACTIONf_angle_d1.41519302
X-RAY DIFFRACTIONf_dihedral_angle_d12.2028792
X-RAY DIFFRACTIONf_chiral_restr0.0712176
X-RAY DIFFRACTIONf_plane_restr0.0092436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4767-3.60090.39091700.28842862X-RAY DIFFRACTION100
3.6009-3.7450.33791150.26472150X-RAY DIFFRACTION75
3.745-3.91530.32381310.2452550X-RAY DIFFRACTION88
3.9153-4.12160.33561380.22322848X-RAY DIFFRACTION100
4.1216-4.37960.30181330.21432891X-RAY DIFFRACTION100
4.3796-4.71730.22561380.18472930X-RAY DIFFRACTION100
4.7173-5.19130.29141580.1792901X-RAY DIFFRACTION100
5.1913-5.94070.27311570.1912890X-RAY DIFFRACTION100
5.9407-7.4780.25081700.1912930X-RAY DIFFRACTION99
7.478-42.46460.18481490.14142991X-RAY DIFFRACTION98

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