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- PDB-2p6n: Human DEAD-box RNA helicase DDX41, helicase domain -

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Basic information

Entry
Database: PDB / ID: 2p6n
TitleHuman DEAD-box RNA helicase DDX41, helicase domain
ComponentsATP-dependent RNA helicase DDX41
KeywordsHYDROLASE / RNA / HELICASE / DEAD / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
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
Probable ATP-dependent RNA helicase DDX41
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKarlberg, T. / Ogg, D. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Karlberg, T. / Ogg, D. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hallberg, B.M. / Hammarstrom, M. / Johansson, I. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Comparative Structural Analysis of Human DEAD-Box RNA Helicases.
Authors: Schutz, P. / Karlberg, T. / van den Berg, S. / Collins, R. / Lehtio, L. / Hogbom, M. / Holmberg-Schiavone, L. / Tempel, W. / Park, H.W. / Hammarstrom, M. / Moche, M. / Thorsell, A.G. / Schuler, H.
History
DepositionMar 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS A MONOMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DDX41
B: ATP-dependent RNA helicase DDX41


Theoretical massNumber of molelcules
Total (without water)42,3452
Polymers42,3452
Non-polymers00
Water00
1
A: ATP-dependent RNA helicase DDX41


Theoretical massNumber of molelcules
Total (without water)21,1721
Polymers21,1721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase DDX41


Theoretical massNumber of molelcules
Total (without water)21,1721
Polymers21,1721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.013, 68.013, 305.604
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 406 - 565 / Label seq-ID: 28 - 187

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is a monomer, the asymmetric unit contains two monomers

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Components

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


Mass: 21172.273 Da / Num. of mol.: 2 / Fragment: HELICASE DOMAIN / Mutation: R525C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX41, ABS / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold pRARE2
References: UniProt: Q9UJV9, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 293 K / pH: 5.5
Details: 25% PEG 3350, 200mM Lithium sulfate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.04005
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2006
Details: DOUBLE CRYSTAL, SI(111) OR SI(311), TOROIDAL MIRROR
RadiationMonochromator: KHOZU, WITH A MCLENNON CONTROLLER CONTAINING A LN2 COOLED SI111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04005 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 13827 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 40 % / Rmerge(I) obs: 0.103 / Rsym value: 0.029 / Net I/σ(I): 35.9
Reflection shellResolution: 2.6→2.8 Å / Redundancy: 41.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 12.6 / Rsym value: 0.084 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0032refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I4I

2i4i


Resolution: 2.6→29.72 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 27.859 / SU ML: 0.266 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.559 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29431 696 5 %RANDOM
Rwork0.24345 ---
obs0.24594 13220 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.341 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 0 0 2481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222518
X-RAY DIFFRACTIONr_bond_other_d0.0030.021691
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9913404
X-RAY DIFFRACTIONr_angle_other_deg0.90934192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3435314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.95625.943106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74715474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.418158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
X-RAY DIFFRACTIONr_nbd_refined0.250.2562
X-RAY DIFFRACTIONr_nbd_other0.1960.21756
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21227
X-RAY DIFFRACTIONr_nbtor_other0.0930.21351
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6351.51733
X-RAY DIFFRACTIONr_mcbond_other0.1231.5636
X-RAY DIFFRACTIONr_mcangle_it0.94222564
X-RAY DIFFRACTIONr_scbond_it1.61231009
X-RAY DIFFRACTIONr_scangle_it2.5484.5840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A926medium positional0.230.5
B1130loose positional0.515
A926medium thermal0.322
B1130loose thermal0.4410
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 49 -
Rwork0.29 929 -
obs--100 %
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)
17.1667-3.4473-1.39776.5293-0.85788.33780.0183-0.11450.42930.7234-0.0013-0.241-0.23540.078-0.0171-0.0312-0.0803-0.01620.0619-0.049-0.2277-19.91133.977191.693
24.03220.8659-0.15563.7860.63666.7715-0.1180.47390.2612-0.29550.14240.0251-0.1877-0.123-0.0244-0.0344-0.05760.02010.09620.0817-0.0934-24.51333.265176.122
37.1827-1.30062.31284.6970.70316.7789-0.04160.018-0.1703-0.153-0.3045-0.37270.20220.46360.346-0.0877-0.05550.03280.11350.0184-0.066-10.99725.528190.719
46.24033.77371.25343.50070.64415.632-0.03281.222-0.3384-0.51250.21120.03870.39960.0914-0.17830.0191-0.04980.07720.2121-0.0391-0.124114.19924.576191.852
54.9156-1.3656-0.47293.35411.19035.6513-0.2117-0.2211-0.05160.11080.24450.11480.1333-0.1278-0.0329-0.0520.03490.06450.03490.0455-0.10259.45225.687207.284
66.87751.1452-1.44366.06410.5554.3295-0.17770.40820.3967-0.18330.2227-0.3175-0.02280.0447-0.045-0.08150.02120.06570.14690.0251-0.045322.66532.89193.409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA406 - 43128 - 53
2X-RAY DIFFRACTION2AA432 - 50854 - 130
3X-RAY DIFFRACTION3AA509 - 568131 - 190
4X-RAY DIFFRACTION4BB406 - 43128 - 53
5X-RAY DIFFRACTION5BB432 - 50854 - 130
6X-RAY DIFFRACTION6BB509 - 565131 - 187

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