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- PDB-3rrn: S. cerevisiae dbp5 l327v bound to gle1 h337r and ip6 -

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Basic information

Entry
Database: PDB / ID: 3rrn
TitleS. cerevisiae dbp5 l327v bound to gle1 h337r and ip6
Components
  • ATP-dependent RNA helicase DBP5
  • Nucleoporin GLE1
KeywordsHYDROLASE / RecA / DEAD-box / HEAT-repeat / 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
ADENOSINE-5'-DIPHOSPHATE / 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 / molecular replacement / Resolution: 4.001 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: 3PEX
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8546
Polymers78,4472
Non-polymers2,4074
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-28 kcal/mol
Surface area30820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.984, 206.984, 206.984
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#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: 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
#4: 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.: 3 / Source method: obtained synthetically / Formula: C6H18O24P6

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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: 4.71 Å3/Da / Density % sol: 73.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 300, 100mM MES, 2% MPD, 10 mM HEPES, 100 mM NaCl, 1 mM DTT, 0.5 mM IP6, 0.5 mM ADP, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.5

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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: Apr 3, 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: 4.001→146.365 Å / Num. all: 12618 / Num. obs: 12618 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 151 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
4-4.227.20.6171.21299918090.617100
4.22-4.477.10.3322.21244117410.332100
4.47-4.787.20.213.61164216270.21100
4.78-5.177.20.1644.61075415040.164100
5.17-5.667.10.1524.9978213870.152100
5.66-6.3370.1345.7894412720.134100
6.33-7.36.90.089.1784911340.08100
7.3-8.956.80.0629.665199570.062100
8.95-12.656.40.02624.148217480.02699.4
12.65-145.8656.70.0269.229274390.02699.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.1 Å48.83 Å
Translation4.1 Å48.83 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
ELVESrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.001→103.492 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.44 / σ(F): 1.38 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 1245 9.87 %Random
Rwork0.2148 ---
obs0.2171 12612 99.91 %-
all-12612 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 97.774 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso max: 261.7 Å2 / Biso mean: 157.7706 Å2 / Biso min: 118.24 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 4.001→103.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 135 0 5577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045917
X-RAY DIFFRACTIONf_angle_d0.6587710
X-RAY DIFFRACTIONf_chiral_restr0.048878
X-RAY DIFFRACTIONf_plane_restr0.002958
X-RAY DIFFRACTIONf_dihedral_angle_d26.5992261
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 (%)
4.0012-4.16140.32061380.283312651403100
4.1614-4.35080.25941340.253212331367100
4.3508-4.58020.24921360.231312381374100
4.5802-4.86720.2631350.22212601395100
4.8672-5.2430.23311350.215712581393100
5.243-5.77050.29711360.244812541390100
5.7705-6.60540.2941450.256712731418100
6.6054-8.32160.22581390.194912681407100
8.3216-103.52660.19061470.17851318146599
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)
16.4537-1.0574-0.07875.7295-0.81516.8531-0.12920.0101-0.4251-0.4476-0.17980.706-0.2712-0.130201.51250.154-0.19951.2501-0.11021.7473-19.561854.786824.5429
25.7889-0.5161-1.17715.2229-1.33296.89270.27130.11510.0095-0.2759-0.11410.3921-0.6032-0.4192-01.72470.1462-0.04691.39640.05041.6717-12.302624.220317.0925
33.3578-1.329-0.27747.62791.12272.7734-0.3032-0.3955-0.09371.19360.35081.0419-0.0389-0.3511-01.81780.27950.43141.72830.31981.8663-20.918220.272145.2784
40.03290.0318-0.03130.0379-0.02220.0372-0.17250.08910.94630.520.1851-0.5169-0.77790.463802.07630.141-0.02461.74870.27751.6714-6.085514.532240.9978
50.0740.0613-0.15730.0708-0.01730.9683-0.5476-1.0683-0.1252-0.0044-0.00710.2817-0.1453-0.2535-0.2221.11150.29390.05961.785-0.1173.46-16.928341.188729.6385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain a and resseq 88:295a88 - 295
2X-RAY DIFFRACTION2chain a and resseq 302:482a302 - 482
3X-RAY DIFFRACTION3chain b and resseq 246:538b246 - 538
4X-RAY DIFFRACTION4chain b and resseq 1b1
5X-RAY DIFFRACTION5chain a and resseq 1a1

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