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- PDB-5elx: S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3 -

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Basic information

Entry
Database: PDB / ID: 5elx
TitleS. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3
Components
  • ATP-dependent RNA helicase DBP5
  • RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
KeywordsHYDROLASE / Fluorescent / Nucleotide / Mant / ADP / RNA helicase
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 transport / mRNA export from nucleus / nuclear pore / translational termination / cytoplasmic stress granule ...cellular bud tip / nuclear pore cytoplasmic filaments / tRNA export from nucleus / ATP-dependent activity, acting on RNA / poly(A)+ mRNA export from nucleus / mRNA transport / mRNA export from nucleus / nuclear pore / translational termination / cytoplasmic stress granule / protein transport / gene expression / nuclear membrane / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / 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
BERYLLIUM TRIFLUORIDE ION / Chem-M2A / NITRATE ION / RNA / ATP-dependent RNA helicase DBP5 / ATP-dependent RNA helicase DBP5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 Å
AuthorsMerchant, M.K. / Modis, Y.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Pi Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5).
Authors: Wong, E.V. / Cao, W. / Voros, J. / Merchant, M. / Modis, Y. / Hackney, D.D. / Montpetit, B. / De La Cruz, E.M.
History
DepositionNov 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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_conn.ptnr2_symmetry

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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)46,4038
Polymers45,6042
Non-polymers7996
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-33 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.082, 91.751, 104.521
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: 43811.590 Da / Num. of mol.: 1 / Fragment: UNP residues 91-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Gene: DBP5, RAT8, SCY_5119 / Production host: Escherichia coli (E. coli)
References: UniProt: A6ZNQ1, UniProt: P20449*PLUS, 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: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 331 molecules

#3: Chemical ChemComp-M2A / [(2~{R},3~{R},4~{R},5~{S})-2-(6-aminopurin-9-yl)-4-oxidanyl-5-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] 2-(methylamino)benzoate


Mass: 560.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N6O11P2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Formula: NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.31 Å3/Da / Density % sol: 46.74 % / Description: Rods
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Mixed 100 nL of the complex at a protein concentration of 16 mg/ml with 100 nL of reservoir solution containing 200 mM Mg(NO3)2 and 18 percent PEG 3350 and incubating 4 days over 100 uL of ...Details: Mixed 100 nL of the complex at a protein concentration of 16 mg/ml with 100 nL of reservoir solution containing 200 mM Mg(NO3)2 and 18 percent PEG 3350 and incubating 4 days over 100 uL of reservoir solution in a sealed chamber.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.81→104.52 Å / Num. obs: 37530 / % possible obs: 99.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.53 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 10.1
Reflection shellResolution: 1.81→1.91 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimless0.1.27data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementResolution: 1.81→52.26 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 1846 4.93 %
Rwork0.175 --
obs0.177 37472 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→52.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 105 51 325 3553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053368
X-RAY DIFFRACTIONf_angle_d1.0564589
X-RAY DIFFRACTIONf_dihedral_angle_d16.4592083
X-RAY DIFFRACTIONf_chiral_restr0.067537
X-RAY DIFFRACTIONf_plane_restr0.005574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.85890.30211460.27842681X-RAY DIFFRACTION100
1.8589-1.91370.29681630.23652731X-RAY DIFFRACTION100
1.9137-1.97540.26241250.21732710X-RAY DIFFRACTION100
1.9754-2.0460.23291340.2022715X-RAY DIFFRACTION100
2.046-2.12790.25951520.19062710X-RAY DIFFRACTION100
2.1279-2.22480.21931360.17442734X-RAY DIFFRACTION100
2.2248-2.34210.21891320.17152762X-RAY DIFFRACTION100
2.3421-2.48880.22481340.17942729X-RAY DIFFRACTION100
2.4888-2.6810.21961410.16912733X-RAY DIFFRACTION100
2.681-2.95080.1941390.17342744X-RAY DIFFRACTION99
2.9508-3.37770.2131430.16592758X-RAY DIFFRACTION99
3.3777-4.25520.15271450.13512767X-RAY DIFFRACTION98
4.2552-52.28230.15831560.15652852X-RAY DIFFRACTION97

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