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- PDB-3g0h: Human dead-box RNA helicase DDX19, in complex with an ATP-analogu... -

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Basic information

Entry
Database: PDB / ID: 3g0h
TitleHuman dead-box RNA helicase DDX19, in complex with an ATP-analogue and RNA
Components
  • 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'
  • ATP-dependent RNA helicase DDX19B
KeywordsHYDROLASE/RNA / PROTEIN-RNA COMPLEX / DBP5 / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Helicase / Hydrolase / Membrane / mRNA transport / Nuclear pore complex / Nucleotide-binding / Nucleus / Phosphoprotein / Protein transport / RNA-binding / Translocation / Transport / polyURACIL / HYDROLASE-RNA COMPLEX
Function / homology
Function and homology information


poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / helicase activity / cytoplasmic stress granule / nuclear envelope / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity ...poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / helicase activity / cytoplasmic stress granule / nuclear envelope / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2170 / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helix non-globular / Helicase conserved C-terminal domain / Special / helicase superfamily c-terminal domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2170 / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helix non-globular / Helicase conserved C-terminal domain / Special / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / ATP-dependent RNA helicase DDX19B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKarlberg, T. / Lehtio, L. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Karlberg, T. / Lehtio, L. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The DEXD/H-box RNA Helicase DDX19 Is Regulated by an {alpha}-Helical Switch.
Authors: Collins, R. / Karlberg, T. / Lehtio, L. / Schutz, P. / van den Berg, S. / Dahlgren, L.G. / Hammarstrom, M. / Weigelt, J. / Schuler, H.
History
DepositionJan 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DDX19B
E: 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7465
Polymers50,1232
Non-polymers6233
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-32 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.570, 81.080, 124.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ATP-dependent RNA helicase DDX19B / DEAD box protein 19B / DEAD box RNA helicase DEAD5


Mass: 48025.246 Da / Num. of mol.: 1 / Fragment: UNP residues 54-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DBP5, DDX19, DDX19B / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold pRARE2
References: UniProt: Q9UMR2, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: RNA chain 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'


Mass: 2098.203 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 14% PEGMME 2000, 0.25M trimethylamine n-oxide, 0.1 M Tris, pH 8, VAPOR DIFFUSION, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEGMME 200011
2trimethylamine n-oxide11
3Tris11
4PEGMME 200012
5trimethylamine n-oxide12
6Tris12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Nov 20, 2008 / Details: monochromator crystals, Si(311) cut and Si(111)
RadiationMonochromator: Liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 12073 / Num. obs: 12073 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.145 / Rsym value: 0.189 / Net I/σ(I): 9.1
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.5 / Num. unique all: 880 / Rsym value: 0.65 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0053refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EWS

3ews


Resolution: 2.7→29.62 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.862 / SU B: 28.618 / SU ML: 0.291 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 600 5 %RANDOM
Rwork0.21722 ---
all0.22014 11474 --
obs0.22014 11474 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.175 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 125 38 0 3388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223453
X-RAY DIFFRACTIONr_bond_other_d0.0010.022350
X-RAY DIFFRACTIONr_angle_refined_deg1.1292.034693
X-RAY DIFFRACTIONr_angle_other_deg0.81135761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0185407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5624.765149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.83315619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9031522
X-RAY DIFFRACTIONr_chiral_restr0.060.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02644
X-RAY DIFFRACTIONr_mcbond_it0.2381.52036
X-RAY DIFFRACTIONr_mcbond_other0.0361.5818
X-RAY DIFFRACTIONr_mcangle_it0.45623295
X-RAY DIFFRACTIONr_scbond_it0.77631417
X-RAY DIFFRACTIONr_scangle_it1.414.51398
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 43 -
Rwork0.269 828 -
obs--99.77 %
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)
11.67150.42932.0780.1950.54152.58770.3355-0.4694-0.1178-0.0607-0.12520.16510.4404-0.591-0.21040.6277-0.0975-0.17730.4910.12350.7228-8.7679-17.4388-39.8642
21.34390.1942-0.21771.3688-0.39951.5377-0.0443-0.2060.0020.0841-0.0665-0.0031-0.06080.02520.11080.00960.0091-0.00170.05670.00950.01393.5915-6.5332-10.8194
31.2336-0.3595-0.08882.8536-0.47141.858-0.0710.1004-0.0494-0.306-0.0359-0.02720.08210.04420.10690.0543-0.01370.0220.0408-0.0070.02477.8145-7.6288-37.4954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 78
2X-RAY DIFFRACTION2A79 - 297
3X-RAY DIFFRACTION3A298 - 469

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