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- PDB-3pev: S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6 -

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Basic information

Entry
Database: PDB / ID: 3pev
TitleS. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6
Components
  • ATP-dependent RNA helicase DBP5
  • Nucleoporin GLE1
KeywordsHYDROLASE / RecA / HEAT / DEAD-box / ATPase / Helicase / mRNA export / Nuclear Pore
Function / homology
Function and homology information


cellular bud tip / regulation of translational termination / tRNA export from nucleus / nuclear pore cytoplasmic filaments / inositol hexakisphosphate binding / ATP-dependent activity, acting on RNA / regulation of translational initiation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / enzyme activator activity ...cellular bud tip / regulation of translational termination / tRNA export from nucleus / nuclear pore cytoplasmic filaments / inositol hexakisphosphate binding / ATP-dependent activity, acting on RNA / regulation of translational initiation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / enzyme activator activity / mRNA export from nucleus / translational termination / nuclear pore / translation initiation factor binding / phospholipid binding / mRNA processing / cytoplasmic stress granule / protein transport / nuclear envelope / nuclear membrane / RNA helicase activity / RNA helicase / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
GLE1-like / mRNA export factor GLE1-like / GLE1-like superfamily / GLE1-like protein / 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 ...GLE1-like / mRNA export factor GLE1-like / GLE1-like superfamily / GLE1-like protein / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 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 / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / ATP-dependent RNA helicase DBP5 / mRNA export factor GLE1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsMontpetit, B. / Thomsen, N.D. / Helmke, K.J. / Seeliger, M.A. / Berger, J.M. / Weis, K.
CitationJournal: Nature / Year: 2011
Title: A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP(6) in mRNA export.
Authors: Montpetit, B. / Thomsen, N.D. / Helmke, K.J. / Seeliger, M.A. / Berger, J.M. / Weis, K.
History
DepositionOct 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Oct 14, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / struct_conn ...chem_comp / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_leaving_atom_flag ..._chem_comp.pdbx_synonyms / _struct_conn.pdbx_leaving_atom_flag / _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 DBP5
B: Nucleoporin GLE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8697
Polymers55,8372
Non-polymers1,0325
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoporin GLE1
hetero molecules

A: ATP-dependent RNA helicase DBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8697
Polymers55,8372
Non-polymers1,0325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666x-y+1,-y+1,-z+11
Buried area2910 Å2
ΔGint-30 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.867, 110.867, 201.914
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 21252.605 Da / Num. of mol.: 1 / Fragment: Dbp5-CTD / Mutation: L327V
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, RNA helicase
#2: Protein Nucleoporin GLE1 / Nuclear pore protein GLE1 / RNA export factor GLE1


Mass: 34583.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BRR3, D1049, GLE1, RSS1, YDL207W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q12315

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Non-polymers , 4 types, 85 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 30% PEG 3350, 100 mM HEPES pH 7.8, 200mM LiS04, 10mM HEPES pH 7.5, 150mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2010
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 26030 / Num. obs: 26030 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1.064 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.594.10.47824081.04794
2.59-2.696.20.51625401.00999.6
2.69-2.827.50.48125621.089100
2.82-2.968.30.39825651.095100
2.96-3.158.40.29325891.087100
3.15-3.398.40.17425791.08199.9
3.39-3.738.30.10626001.01599.8
3.73-4.278.20.06626461.07299.9
4.27-5.3880.05926651.06299.9
5.38-507.40.03428761.05899.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ELVESrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.499→48.007 Å / Occupancy max: 1 / Occupancy min: 0.71 / SU ML: 0.31 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1293 4.98 %Random
Rwork0.2021 ---
all0.2039 25940 --
obs0.2039 25940 99.14 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.855 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 161.2 Å2 / Biso mean: 61.0358 Å2 / Biso min: 35.65 Å2
Baniso -1Baniso -2Baniso -3
1--19.4889 Å2-0 Å20 Å2
2---19.4889 Å20 Å2
3---38.9778 Å2
Refinement stepCycle: LAST / Resolution: 2.499→48.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3807 0 59 80 3946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043937
X-RAY DIFFRACTIONf_angle_d0.7085330
X-RAY DIFFRACTIONf_chiral_restr0.053602
X-RAY DIFFRACTIONf_plane_restr0.002666
X-RAY DIFFRACTIONf_dihedral_angle_d20.5011506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.499-2.59910.34641310.31762543267494
2.5991-2.71730.35111420.277426742816100
2.7173-2.86060.29181410.250226962837100
2.8606-3.03980.30851420.233627092851100
3.0398-3.27440.27661430.228427302873100
3.2744-3.60390.2761440.211927372881100
3.6039-4.12510.23041440.1827652909100
4.1251-5.19620.18741490.156728042953100
5.1962-48.01570.18411570.18929893146100
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)
12.53160.1418-2.38282.309-0.95412.734-0.0010.04910.1177-0.11350.06320.2090.1159-0.3174-0.00030.46120.006-0.05750.5571-0.08410.674917.870261.9268105.3973
22.48910.5372-0.3722.2688-1.41611.7922-0.02450.0199-0.31710.093-0.0859-0.66560.33380.3837-0.00020.6508-0.0284-0.03670.6863-0.12230.792623.608253.8873115.7017
32.7252-0.7727-0.11122.91931.19272.5310.03-0.0470.84440.0440.1132-0.1658-0.07350.0762-0.00010.4308-0.0164-0.01580.4765-0.07430.618342.950971.5307100.6647
44.4988-0.33440.55273.23460.37922.02760.02490.24160.072-0.2660.06720.04560.0317-0.0843-00.47130.0222-0.01160.533-0.07260.404147.497655.077687.6943
50.21820.11840.13641.7502-0.55930.32330.2399-1.0098-0.58440.7470.16890.15971.4607-0.20940.00560.5433-0.0190.00060.7389-0.19870.57647.028962.9383110.2915
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain a and resseq 303:389a303 - 389
2X-RAY DIFFRACTION2chain a and resseq 390:482a390 - 482
3X-RAY DIFFRACTION3chain b and resseq 244:379b244 - 379
4X-RAY DIFFRACTION4chain b and resseq 380:538b380 - 538
5X-RAY DIFFRACTION5chain cc0

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