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- PDB-3rrm: S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp -

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Basic information

Entry
Database: PDB / ID: 3rrm
TitleS. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp
Components
  • ATP-dependent RNA helicase DBP5
  • Nucleoporin GLE1
  • Nucleoporin NUP159
KeywordsHYDROLASE / RecA / DEAD-box / HEAT-repeat / beta-propeller / ATPase / Helicase / mRNA-export / Nuclear Pore
Function / homology
Function and homology information


: / nuclear pore central transport channel / adenyl-nucleotide exchange factor activity / nuclear pore localization / cellular bud tip / regulation of translational termination / tRNA export from nucleus / nuclear pore cytoplasmic filaments / inositol hexakisphosphate binding / ATP-dependent activity, acting on RNA ...: / nuclear pore central transport channel / adenyl-nucleotide exchange factor activity / nuclear pore localization / cellular bud tip / regulation of translational termination / tRNA export from nucleus / nuclear pore cytoplasmic filaments / inositol hexakisphosphate binding / ATP-dependent activity, acting on RNA / structural constituent of nuclear pore / regulation of translational initiation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / NLS-bearing protein import into nucleus / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / enzyme activator activity / mRNA export from nucleus / translational termination / translation initiation factor binding / nuclear pore / protein export from nucleus / phospholipid binding / mRNA processing / cytoplasmic stress granule / transcription corepressor activity / protein transport / nuclear envelope / nuclear membrane / RNA helicase activity / molecular adaptor activity / RNA helicase / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
GLE1-like / Nucleoporin Nup159/Nup146, N-terminal / Nucleoporin or Nuclear pore complex subunit NUP214=Nup159 / 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. ...GLE1-like / Nucleoporin Nup159/Nup146, N-terminal / Nucleoporin or Nuclear pore complex subunit NUP214=Nup159 / 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. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / ATP-dependent RNA helicase DBP5 / Nucleoporin NUP159 / mRNA export factor GLE1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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 InsP6 in mRNA export.
Authors: Montpetit, B. / Thomsen, N.D. / Helmke, K.J. / Seeliger, M.A. / Berger, J.M. / Weis, K.
History
DepositionApr 29, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionMay 18, 2011ID: 3PEZ
Revision 1.0May 18, 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_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_ref_seq_dif.details ..._chem_comp.pdbx_synonyms / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Nucleoporin NUP159
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5956
Polymers121,4843
Non-polymers1,1123
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-23 kcal/mol
Surface area30520 Å2
Unit cell
Length a, b, c (Å)186.912, 67.982, 132.392
Angle α, β, γ (deg.)90.000, 127.520, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABC

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


Mass: 44171.973 Da / Num. of mol.: 1 / Fragment: unp residues 91-482 / 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: 34274.719 Da / Num. of mol.: 1 / Fragment: unp residues 244-538 / Mutation: H337R
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
#3: Protein Nucleoporin NUP159 / Nuclear pore protein NUP159


Mass: 43037.168 Da / Num. of mol.: 1 / Fragment: unp residues 2-387
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP158, NUP159, RAT7, YIL115C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P40477

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Non-polymers , 3 types, 3 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 200 mM KOAc, 20 mM sarcosine, 10 mM HEPES, 100 mM NaCl, 1 mM DTT, 0.5 mM IP6, 10 mM MgCl2, 1 mM ADP, 5% glycerol, pH 7.5, 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: Jul 17, 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: 2.9→50 Å / Num. all: 29961 / Num. obs: 29961 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.101 / Χ2: 1.061 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-33.50.66829661.015199.7
3-3.123.60.52829851.087199.8
3.12-3.273.60.35829691.097199.8
3.27-3.443.70.24529771.079199.9
3.44-3.653.80.17329761.0911100
3.65-3.943.80.11729841.0581100
3.94-4.333.90.08129911.097199.8
4.33-4.963.90.05930001.035199.8
4.96-6.243.90.06730221.061199.9
6.24-503.80.03630910.99199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ELVESrefinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→48.268 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 0 / Phase error: 28.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 1516 5.06 %Random
Rwork0.2285 ---
obs0.2303 29959 98.84 %-
all-29959 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.733 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso max: 126.46 Å2 / Biso mean: 61.2709 Å2 / Biso min: 34.16 Å2
Baniso -1Baniso -2Baniso -3
1--13.0547 Å20 Å26.3592 Å2
2---1.2471 Å20 Å2
3---14.3017 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8259 0 64 0 8323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028480
X-RAY DIFFRACTIONf_angle_d0.5611497
X-RAY DIFFRACTIONf_chiral_restr0.0371327
X-RAY DIFFRACTIONf_plane_restr0.0021464
X-RAY DIFFRACTIONf_dihedral_angle_d16.9113213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8753-2.96810.35561170.33672290240788
2.9681-3.07420.36281290.32225962725100
3.0742-3.19730.29821400.299825922732100
3.1973-3.34270.31871460.278625792725100
3.3427-3.51890.3051420.256225902732100
3.5189-3.73930.22271120.230426482760100
3.7393-4.02790.27551440.215225892733100
4.0279-4.4330.22831350.19426232758100
4.433-5.07390.23371490.177825992748100
5.0739-6.39020.241480.223426362784100
6.3902-48.27450.23211540.205427012855100
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)
12.9201-0.03831.33831.7817-0.04424.27610.38310.1323-0.1727-0.2691-0.40640.26480.7004-0.438500.8512-0.0377-0.08670.5829-0.12370.546777.0592-25.517553.2605
23.8653-1.14660.41454.3833-0.43262.3805-0.025-0.26890.22710.2338-0.1842-0.21310.0645-0.0909-0.00010.4318-0.0137-0.03040.4217-0.07870.65393.5327-9.263527.2218
34.98830.981-1.24882.4118-0.73122.5409-0.01760.25650.1686-0.14490.05450.02790.1239-0.360900.40030.0506-0.06620.4939-0.01550.433965.6947-9.219416.6317
44.0931-0.15260.22721.8850.39852.50240.0629-0.4480.20040.1972-0.1909-0.02570.0832-0.1828-0.00010.5046-0.08550.06470.4305-0.05840.437889.3567-7.684.8625
50.00250.0005-0.00270.0007-0.00110.0018-0.3132-0.0346-0.26880.0836-0.3837-0.2734-0.07910.07760.00060.97920.2650.09362.410.16130.856478.037-20.984438.6338
60.09780.0352-0.01580.0158-0.00810.031-0.12270.0809-0.16810.1962-0.1309-0.49550.22660.1852-0.0010.5899-0.08210.12970.8343-0.10410.706877.9757-12.36916.0971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain a and resseq 90:295a90 - 295
2X-RAY DIFFRACTION2chain a and resseq 299:482a299 - 482
3X-RAY DIFFRACTION3chain b and resseq 244:538b244 - 538
4X-RAY DIFFRACTION4chain cc0
5X-RAY DIFFRACTION5chain a and resseq 1a1
6X-RAY DIFFRACTION6chain b and resseq 1b1

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