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- PDB-3gfp: Structure of the C-terminal domain of the DEAD-box protein Dbp5 -

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Basic information

Entry
Database: PDB / ID: 3gfp
TitleStructure of the C-terminal domain of the DEAD-box protein Dbp5
ComponentsDEAD box protein 5
KeywordsHYDROLASE / mRNA export / ATPase / RecA-fold / ATP-binding / Helicase / Membrane / mRNA transport / Nuclear pore complex / Nucleotide-binding / Nucleus / Phosphoprotein / Protein transport / RNA-binding / Translocation / Transport
Function / homology
Function and homology information


cellular bud tip / nuclear pore cytoplasmic filaments / tRNA export from nucleus / ATP-dependent activity, acting on RNA / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / translational termination / cytoplasmic stress granule / protein transport / nuclear membrane ...cellular bud tip / nuclear pore cytoplasmic filaments / tRNA export from nucleus / ATP-dependent activity, acting on RNA / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / translational termination / cytoplasmic stress granule / protein transport / nuclear membrane / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / 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-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / 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
ATP-dependent RNA helicase DBP5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsErzberger, J.P. / Dossani, Z.Y. / Weirich, C.S. / Weis, K. / Berger, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of the C-terminus of the mRNA export factor Dbp5 reveals the interaction surface for the ATPase activator Gle1
Authors: Dossani, Z.Y. / Weirich, C.S. / Erzberger, J.P. / Berger, J.M. / Weis, K.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DEAD box protein 5


Theoretical massNumber of molelcules
Total (without water)21,3681
Polymers21,3681
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.423, 82.423, 56.578
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-2-

HOH

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Components

#1: Protein DEAD box protein 5 / / ATP-dependent RNA helicase DBP5 / Helicase CA5/6 / Ribonucleic acid-trafficking protein 8


Mass: 21367.734 Da / Num. of mol.: 1 / Fragment: Helicase C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DBP5, RAT8, YOR046C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL
References: UniProt: P20449, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M Na/K HPO4, 100mM Na cacodylate pH 6.5, 8% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9795,1.0332,1.11588
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 15, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.03321
31.115881
ReflectionResolution: 1.7→56.6 Å / Num. all: 24212 / Num. obs: 24212 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.04

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.32 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22999 1016 5 %RANDOM
Rwork0.1913 ---
obs0.19315 19340 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.957 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0.41 Å20 Å2
2---0.82 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 0 153 1575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221451
X-RAY DIFFRACTIONr_angle_refined_deg0.9561.9591959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2195180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.50424.24266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02815268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4911510
X-RAY DIFFRACTIONr_chiral_restr0.0730.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021069
X-RAY DIFFRACTIONr_nbd_refined0.2070.2738
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21022
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.222
X-RAY DIFFRACTIONr_mcbond_it0.8511.5919
X-RAY DIFFRACTIONr_mcangle_it1.25121454
X-RAY DIFFRACTIONr_scbond_it2.0113588
X-RAY DIFFRACTIONr_scangle_it2.9654.5505
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 80 -
Rwork0.23 1404 -
obs--99.73 %
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)
11.0484-0.21510.19011.3285-0.0990.7842-0.12960.06420.10110.0240.0543-0.0772-0.090.06490.0753-0.0285-0.0184-0.0466-0.03260.0337-0.0399-19.9794-19.9272-8.413
20.4479-0.25930.16241.0719-0.10580.411-0.10490.07780.04720.01560.0276-0.0478-0.04110.01620.0773-0.0344-0.009-0.0237-0.00960.0351-0.0479-21.7709-20.7604-9.6589
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A300 - 479
2X-RAY DIFFRACTION2A1 - 153

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