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- PDB-5gvr: Crystal structure of the DDX41 DEAD domain in an apo closed form -

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Basic information

Entry
Database: PDB / ID: 5gvr
TitleCrystal structure of the DDX41 DEAD domain in an apo closed 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 / mRNA binding / apoptotic process / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / 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 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 ...DDX41, DEAD-box helicase domain / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / Probable ATP-dependent RNA helicase DDX41
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsOmura, H. / Oikawa, D. / Nakane, T. / Kato, M. / Ishii, R. / Goto, Y. / Suga, H. / Ishitani, R. / Tokunaga, F. / Nureki, O.
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 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3082
Polymers26,1741
Non-polymers1341
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.830, 81.830, 69.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 26174.188 Da / Num. of mol.: 1 / Fragment: UNP residues 169-402
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: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: DL-malic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→50.01 Å / Num. obs: 41380 / % possible obs: 99.9 % / Redundancy: 10.34 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 18.4
Reflection shellResolution: 1.5→1.51 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
PHASERphasing
REFMACmodel building
XDSdata scaling
XDSdata reduction
XDSdata processing
XDSdata extraction
XDSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FE2

3fe2


Resolution: 1.5→50.01 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.628 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20806 2173 5 %RANDOM
Rwork0.18069 ---
obs0.18205 41380 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.416 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.4 Å2-0 Å2
2---0.8 Å20 Å2
3---2.58 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 9 114 1949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191869
X-RAY DIFFRACTIONr_bond_other_d0.0020.021898
X-RAY DIFFRACTIONr_angle_refined_deg2.1822.0032510
X-RAY DIFFRACTIONr_angle_other_deg1.08934384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.785233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30622.60969
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62915361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7371515
X-RAY DIFFRACTIONr_chiral_restr0.1280.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212028
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02397
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_it2.9692.626935
X-RAY DIFFRACTIONr_mcbond_other2.9622.623934
X-RAY DIFFRACTIONr_mcangle_it4.343.9211167
X-RAY DIFFRACTIONr_mcangle_other4.3393.9261168
X-RAY DIFFRACTIONr_scbond_it4.4693.238934
X-RAY DIFFRACTIONr_scbond_other4.4593.235931
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6264.5911342
X-RAY DIFFRACTIONr_long_range_B_refined8.35933.3362144
X-RAY DIFFRACTIONr_long_range_B_other8.39932.9822101
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 157 -
Rwork0.33 3052 -
obs--99.41 %

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