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- PDB-5gvs: Crystal structure of the DDX41 DEAD domain in an apo open form -

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Basic information

Entry
Database: PDB / ID: 5gvs
TitleCrystal structure of the DDX41 DEAD domain in an apo open form
ComponentsProbable ATP-dependent RNA helicase DDX41
KeywordsHYDROLASE / ATPase / DEAD box protein
Function / homology
Function and homology information


STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / catalytic step 2 spliceosome / Regulation of innate immune responses to cytosolic DNA / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / cell population proliferation / RNA helicase activity / cell differentiation ...STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / catalytic step 2 spliceosome / Regulation of innate immune responses to cytosolic DNA / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / cell population proliferation / RNA helicase activity / cell differentiation / RNA helicase / apoptotic process / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol
Similarity search - Function
DDX41, DEAD-box helicase domain / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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 ...DDX41, DEAD-box helicase domain / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable ATP-dependent RNA helicase DDX41
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOmura, H. / Oikawa, D. / Nakane, T. / Kato, M. / Ishii, R. / Goto, Y. / Suga, H. / Ishitani, R. / Tokunaga, F. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: Sci Rep / Year: 2016
Title: Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide
Authors: Omura, H. / Oikawa, D. / Nakane, T. / Kato, M. / Ishii, R. / Ishitani, R. / Tokunaga, F. / Nureki, O.
History
DepositionSep 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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: Probable ATP-dependent RNA helicase DDX41
B: Probable ATP-dependent RNA helicase DDX41
C: Probable ATP-dependent RNA helicase DDX41
D: Probable ATP-dependent RNA helicase DDX41


Theoretical massNumber of molelcules
Total (without water)103,5554
Polymers103,5554
Non-polymers00
Water4,197233
1
A: Probable ATP-dependent RNA helicase DDX41


Theoretical massNumber of molelcules
Total (without water)25,8891
Polymers25,8891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ATP-dependent RNA helicase DDX41


Theoretical massNumber of molelcules
Total (without water)25,8891
Polymers25,8891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable ATP-dependent RNA helicase DDX41


Theoretical massNumber of molelcules
Total (without water)25,8891
Polymers25,8891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Probable ATP-dependent RNA helicase DDX41


Theoretical massNumber of molelcules
Total (without water)25,8891
Polymers25,8891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.188, 50.960, 202.599
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
Probable ATP-dependent RNA helicase DDX41 / DEAD box protein 41 / DEAD box protein abstrakt homolog


Mass: 25888.863 Da / Num. of mol.: 4 / Fragment: UNP residues 169-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX41, ABS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJV9, RNA helicase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: tri-ammonium citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.979 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→49.41 Å / Num. obs: 36258 / % possible obs: 76.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.202 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.27 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
PHENIXmodel building
MOSFLMdata collection
MOSFLMdata extraction
MOSFLMdata processing
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GVR

5gvr


Resolution: 2.2→49.41 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.882 / SU B: 8.371 / SU ML: 0.204 / Cross valid method: FREE R-VALUE / ESU R: 0.479 / ESU R Free: 0.298 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27487 1824 5 %RANDOM
Rwork0.20722 ---
obs0.21071 34370 76.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.482 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å2-0.38 Å2
2---1.42 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 0 0 233 6706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196583
X-RAY DIFFRACTIONr_bond_other_d0.0020.026708
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9978828
X-RAY DIFFRACTIONr_angle_other_deg1.02315462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9975820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4422.5248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.989151298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1571556
X-RAY DIFFRACTIONr_chiral_restr0.0910.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217128
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021424
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9442.2853298
X-RAY DIFFRACTIONr_mcbond_other1.9432.2853297
X-RAY DIFFRACTIONr_mcangle_it3.3963.4194112
X-RAY DIFFRACTIONr_mcangle_other3.3963.4194113
X-RAY DIFFRACTIONr_scbond_it1.9912.5813285
X-RAY DIFFRACTIONr_scbond_other1.9912.5813286
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3753.7384716
X-RAY DIFFRACTIONr_long_range_B_refined6.05327.1117142
X-RAY DIFFRACTIONr_long_range_B_other6.04227.0877096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 120 -
Rwork0.279 2536 -
obs--76.83 %

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