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- PDB-3peu: S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6 -

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Basic information

Entry
Database: PDB / ID: 3peu
TitleS. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R 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 / translation initiation factor binding / nuclear pore / 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 / MAD / Resolution: 2.6 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 1.2Aug 10, 2011Group: Refinement description
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 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)56,8887
Polymers55,8562
Non-polymers1,0325
Water1,02757
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)56,8887
Polymers55,8562
Non-polymers1,0325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666x-y+1,-y+1,-z+11
Buried area2880 Å2
ΔGint-29 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.356, 110.356, 201.453
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,H337R
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: 34602.980 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, 62 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.: 57 / 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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG 3350, 100 mM HEPES pH 8.0, 50 mM NaOAc, 200mM LiS04, 10 mM HEPES pH 7.5, 100mM 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: 0.9796, 0.9798, 1.020
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2009
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97981
31.021
ReflectionRedundancy: 15.5 % / Av σ(I) over netI: 18.95 / Number: 582758 / Rmerge(I) obs: 0.129 / Χ2: 1.07 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 37575 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.815099.610.0470.94215.3
4.625.8110010.0881.06515.4
4.034.6210010.0771.06415.6
3.664.0310010.0991.07115.6
3.43.6610010.1481.05815.6
3.23.410010.2151.07415.6
3.043.210010.3121.0815.6
2.913.0410010.4711.13715.6
2.82.9110010.5891.10915.6
2.72.810010.7461.07615.2
ReflectionResolution: 2.6→50 Å / Num. all: 42284 / Num. obs: 42284 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.1 / Χ2: 1.025 / Net I/σ(I): 18.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.697.40.6942660.9681100
2.69-2.87.60.56441951.0151100
2.8-2.937.60.41742291.0441100
2.93-3.087.60.30842411.0841100
3.08-3.287.60.20242141.0961100
3.28-3.537.60.12542261.071100
3.53-3.887.60.08142351.0221100
3.88-4.457.60.06142240.996199.9
4.45-5.67.40.06742200.978199.8
5.6-507.50.03542340.976199.3

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.6 Å / D res low: 1000 Å / FOM : 0.51 / Reflection: 23060
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.97967-8.6
3 wavelength120.97973.75-9.04
3 wavelength131.01990.31-3.37
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se38.0990.2070.4340.9811.066
2Se36.7090.1510.4250.5160.975
3Se600.2680.5490.9281.084
4Se600.1130.2990.5440.92
5Se600.0750.3780.0971.034
6Se600.0750.4450.211.098
7Se600.0780.4260.6260.848
8Se600.0420.4060.2170.898
9Se58.2450.0840.4370.2480.71
10Se600.1260.3160.9470.951
11Se600.0460.5040.2610.85
Phasing MAD shell
Resolution (Å)FOM Reflection
9.49-10000.881161
5.95-9.490.851961
4.64-5.950.792454
3.92-4.640.722862
3.46-3.920.613221
3.13-3.460.463546
2.88-3.130.283819
2.68-2.880.084036

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.14phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ELVESrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→48.393 Å / Occupancy max: 1 / Occupancy min: 0.71 / SU ML: 0.34 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 1974 4.98 %Random
Rwork0.1871 ---
all0.1884 39606 --
obs0.1884 39606 93.7 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.931 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 129.28 Å2 / Biso mean: 58.1632 Å2 / Biso min: 31.38 Å2
Baniso -1Baniso -2Baniso -3
1--14.8169 Å2-0 Å20 Å2
2---14.8169 Å20 Å2
3---29.6337 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 59 57 3924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033937
X-RAY DIFFRACTIONf_angle_d0.6775329
X-RAY DIFFRACTIONf_chiral_restr0.047602
X-RAY DIFFRACTIONf_plane_restr0.002666
X-RAY DIFFRACTIONf_dihedral_angle_d21.9681509
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5996-2.66460.33051210.29172404252583
2.6646-2.73660.29891350.27932390252584
2.7366-2.81710.36311390.26482449258886
2.8171-2.90810.30071360.26012531266788
2.9081-3.0120.30921310.24282548267989
3.012-3.13250.2491350.23992697283294
3.1325-3.27510.25971500.20842731288195
3.2751-3.44770.21231430.20322801294497
3.4477-3.66370.22671440.17962816296098
3.6637-3.94640.18611460.15932865301199
3.9464-4.34330.19911480.15362829297799
4.3433-4.97130.15231510.140828583009100
4.9713-6.26110.20861430.18252851299499
6.2611-48.40110.1571520.16362862301499
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)
12.6353-0.184-1.95252.7534-1.37442.90370.05190.07460.1674-0.03410.02850.19460.1092-0.3855-00.4106-0.0149-0.04370.5471-0.09910.618917.946461.7387105.2015
22.21721.0037-0.84382.0309-1.63651.8307-0.0135-0.0962-0.31490.0614-0.0851-0.67920.30880.377300.6186-0.0049-0.02750.666-0.12470.713823.727653.6898115.5027
32.5198-0.6014-0.10292.62431.00712.63060.0235-0.12180.78720.06430.1336-0.135-0.11260.03500.3955-0.0263-0.02340.4342-0.06310.613742.951571.2632100.3666
44.1014-0.04990.5622.86870.2572.01570.03310.27870.0406-0.20840.08760.03730.0658-0.0859-00.43680.0247-0.00910.4962-0.04980.359247.441854.819887.4052
50.0069-0.00540.00070.0045-0.00280.0250.402-1.1-0.66071.10810.10860.07070.7526-0.367200.5499-0.0208-0.05490.7611-0.15540.71247.202962.7045110.0244
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 B AND RESSEQ 3001B3001

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