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- PDB-3pew: S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3 -

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Basic information

Entry
Database: PDB / ID: 3pew
TitleS. cerevisiae Dbp5 L327V 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. / 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 / 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. / 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 / 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 / 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 / molecular replacement / Resolution: 1.501 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)46,84012
Polymers45,9642
Non-polymers87610
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-37 kcal/mol
Surface area17510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.309, 90.810, 105.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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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: 44171.973 Da / Num. of mol.: 1 / 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: 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 , 5 types, 542 molecules

#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-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 / Nitrate


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
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: 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: 1.5→50 Å / Num. all: 64800 / Num. obs: 64800 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.03 / Net I/σ(I): 25.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.553.90.32863081.02597.7
1.55-1.626.20.31664851.03999.9
1.62-1.697.50.2664641.019100
1.69-1.787.60.19764921.045100
1.78-1.897.60.1464831.058100
1.89-2.047.60.10165281.07100
2.04-2.247.20.07365190.99299.6
2.24-2.567.10.05765331.03899.4
2.56-3.237.20.05166531.005100
3.23-506.60.0363350.99891.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.69 Å
Translation2.5 Å29.69 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.2.0phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ELVESrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.501→34.36 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.17 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1893 3232 5 %Random
Rwork0.1649 ---
all0.1661 64601 --
obs0.1661 64601 98.47 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.313 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 51.23 Å2 / Biso mean: 17.5475 Å2 / Biso min: 6.02 Å2
Baniso -1Baniso -2Baniso -3
1--3.5766 Å20 Å2-0 Å2
2--8.1651 Å2-0 Å2
3----4.5885 Å2
Refinement stepCycle: LAST / Resolution: 1.501→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3071 105 54 532 3762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133494
X-RAY DIFFRACTIONf_angle_d1.5034790
X-RAY DIFFRACTIONf_chiral_restr0.084568
X-RAY DIFFRACTIONf_plane_restr0.009599
X-RAY DIFFRACTIONf_dihedral_angle_d14.4761414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5011-1.52350.26971300.24542499262993
1.5235-1.54730.28951380.24252634277299
1.5473-1.57270.23451410.21432668280999
1.5727-1.59980.22681390.200126522791100
1.5998-1.62890.21581430.178426922835100
1.6289-1.66020.2011370.171726512788100
1.6602-1.69410.18071450.160227262871100
1.6941-1.73090.18991380.162726422780100
1.7309-1.77120.21111420.153526932835100
1.7712-1.81550.19031410.153726572798100
1.8155-1.86460.18611410.155326872828100
1.8646-1.91940.20341420.16342666280899
1.9194-1.98140.20361400.163726872827100
1.9814-2.05220.20731410.161826702811100
2.0522-2.13440.18391440.166127202864100
2.1344-2.23150.1721390.16012671281099
2.2315-2.34910.19221400.16552654279498
2.3491-2.49620.16881430.160827082851100
2.4962-2.68890.211440.161427222866100
2.6889-2.95940.18751440.162427302874100
2.9594-3.38730.18571440.160227572901100
3.3873-4.26630.14421210.13942264238581
4.2663-34.3690.18751550.171529193074100
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)
10.7656-0.0017-0.11970.6958-0.0030.64750.004-0.0976-0.03970.0478-0.0133-0.00210.04210.000600.0675-0.0037-0.00160.06330.00650.0604-3.5089-8.502141.1998
20.4886-0.00570.04830.921-0.3081.5016-0.02650.0356-0.0437-0.07350.0134-0.01770.0476-0.024400.0721-0.01510.00640.0611-0.00550.0786-5.6599-13.910313.217
30.00030.00050.00080.005-0.00370.0079-0.0481-0.0157-0.05450.04080.0145-0.01210.02970.006-00.1018-0.00450.00120.1018-0.00330.12423.0377-5.17729.1344
40.07710.0197-0.01310.09610.0740.07860.0287-0.1655-0.31780.06250.14940.15680.254-0.7199-00.1513-0.03630.00430.20990.02060.1693-15.3398-22.355329.5862
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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