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- PDB-3pey: S. cerevisiae Dbp5 bound to RNA and ADP BeF3 -

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Basic information

Entry
Database: PDB / ID: 3pey
TitleS. cerevisiae Dbp5 bound to RNA and ADP BeF3
Components
  • ATP-dependent RNA helicase DBP5
  • RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
KeywordsHYDROLASE/RNA / RecA / DEAD-box / ATPase / Helicase / mRNA-export / Nuclear Pore / HYDROLASE-RNA complex
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. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / NITRATE ION / RNA / ATP-dependent RNA helicase DBP5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 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 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,88412
Polymers45,9782
Non-polymers90610
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-40 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.136, 92.206, 104.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / RNA chain , 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: 44186.000 Da / Num. of mol.: 1
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: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Mass: 1792.037 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 6 types, 503 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#6: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 200 mM MgNO3, 10 mM HEPES pH 7.5, 100 mM NaCl, 1mM DTT, 0.5 mM IP6, 5 mM MgCl2, 1 mM ADP, 3 mM BeCl2, 15 mM NaF, 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: Jun 18, 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: 1.4→50 Å / Num. all: 76028 / Num. obs: 76028 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.04 / Χ2: 1.041 / Net I/σ(I): 26.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.452.30.43553491.05167
1.45-1.512.60.31967941.05785.3
1.51-1.583.50.23377421.0797
1.58-1.663.70.17978391.07897.8
1.66-1.763.80.12178541.06597.7
1.76-1.93.80.08178281.02597.5
1.9-2.093.80.05379221.02198
2.09-2.393.80.03680661.01799.5
2.39-3.023.90.03981650.99199.6
3.02-503.90.01884691.05999.5

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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: 1.401→45.467 Å / Occupancy max: 1 / Occupancy min: 0.12 / SU ML: 0.18 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 3757 4.95 %Random
Rwork0.1602 ---
all0.1612 75947 --
obs0.1612 75947 93.93 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.227 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 61.7 Å2 / Biso mean: 16.3332 Å2 / Biso min: 4.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.4548 Å20 Å2-0 Å2
2--4.8308 Å20 Å2
3----2.376 Å2
Refinement stepCycle: LAST / Resolution: 1.401→45.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 105 56 493 3726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163588
X-RAY DIFFRACTIONf_angle_d1.5164894
X-RAY DIFFRACTIONf_chiral_restr0.094570
X-RAY DIFFRACTIONf_plane_restr0.009617
X-RAY DIFFRACTIONf_dihedral_angle_d15.6381450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.401-1.41870.3405780.29761708178661
1.4187-1.43740.2798930.26791907200068
1.4374-1.45710.26841050.25562110221575
1.4571-1.47790.2581160.23642336245283
1.4779-1.50.22631210.21472473259487
1.5-1.52340.27181310.20232609274093
1.5234-1.54840.23561450.18032743288897
1.5484-1.57510.22631480.17562728287698
1.5751-1.60370.1911470.16482763291098
1.6037-1.63460.19541430.16122768291198
1.6346-1.6680.17641390.15332753289298
1.668-1.70420.18621440.15122753289798
1.7042-1.74390.18841430.14862775291898
1.7439-1.78750.18021460.14372763290998
1.7875-1.83580.15141430.14152767291098
1.8358-1.88980.18331510.14872735288697
1.8898-1.95080.17341430.14652782292598
1.9508-2.02060.17921550.15462787294298
2.0206-2.10150.16421520.16362790294298
2.1015-2.19710.19521430.16112825296899
2.1971-2.31290.1791480.143828492997100
2.3129-2.45780.16041520.152528533005100
2.4578-2.64760.17951490.15882859300899
2.6476-2.9140.17711560.162328683024100
2.914-3.33550.16331490.152828923041100
3.3355-4.20190.13921570.132429493106100
4.2019-45.49050.18261600.17243045320599
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)
10.3967-0.0434-0.2050.3722-0.01160.26960.0032-0.0844-0.01320.0279-0.0081-0.01140.00870.0067-00.0605-0.002-0.00080.05460.01490.0554-3.4702-9.012841.4606
20.1415-0.0485-0.04740.4493-0.1170.6498-0.02290.0578-0.0179-0.04410.0072-0.02340.0196-0.0045-0.0050.0622-0.01170.00710.0601-0.00160.0622-5.4034-13.988413.36
30.00640.00480.00240.00360.00180.00090.0361-0.0148-0.03820.03130.0376-0.0289-0.0111-0.036600.088-0.00050.00370.07250.00020.10273.2363-5.379829.1381
40.01230.0102-0.00060.00960.00170.0041-0.0554-0.0557-0.11130.04660.03910.11350.0993-0.252600.1226-0.02390.01420.12860.01150.1414-15.2172-22.28729.5945
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 296:481a296 - 481
3X-RAY DIFFRACTION3chain a and resseq 1000:1002a1000 - 1002
4X-RAY DIFFRACTION4chain bb0

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