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- PDB-4ljy: Crystal structure of RNA splicing effector Prp5 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 4ljy
TitleCrystal structure of RNA splicing effector Prp5 in complex with ADP
ComponentsPre-mRNA-processing ATP-dependent RNA helicase PRP5
KeywordsHYDROLASE / Prp5 / DEAD box / RNA splicing
Function / homology
Function and homology information


mRNA branch site recognition / ATP-dependent activity, acting on RNA / commitment complex / mRNA splicing, via spliceosome / nucleic acid binding / RNA helicase activity / RNA helicase / ATP hydrolysis activity / ATP binding / nucleus
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 / Pre-mRNA-processing ATP-dependent RNA helicase PRP5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsZhang, Z.-M. / Li, J. / Yang, F. / Xu, Y. / Zhou, J.
CitationJournal: Cell Rep / Year: 2013
Title: Crystal structure of Prp5p reveals interdomain interactions that impact spliceosome assembly.
Authors: Zhang, Z.M. / Yang, F. / Zhang, J. / Tang, Q. / Li, J. / Gu, J. / Zhou, J. / Xu, Y.Z.
History
DepositionJul 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA-processing ATP-dependent RNA helicase PRP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4035
Polymers55,7151
Non-polymers6884
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.598, 86.598, 125.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1015-

HOH

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Components

#1: Protein Pre-mRNA-processing ATP-dependent RNA helicase PRP5


Mass: 55715.066 Da / Num. of mol.: 1 / Fragment: UNP residues 206-698
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PRP5, RNA5, YBR237W, YBR1603 / Production host: Escherichia coli (E. coli) / References: UniProt: P21372, RNA helicase
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, 22.5% PEG 4000, 0.6M NaCl , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 37859

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→43.299 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8515 / SU ML: 0.25 / σ(F): 0 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1829 5.24 %RANDOM
Rwork0.2006 ---
obs0.2019 34921 98.5 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.341 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 123.89 Å2 / Biso mean: 35.9208 Å2 / Biso min: 19.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.7765 Å20 Å2-0 Å2
2--2.7765 Å20 Å2
3----5.553 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 44 250 3801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073653
X-RAY DIFFRACTIONf_angle_d1.1394944
X-RAY DIFFRACTIONf_dihedral_angle_d15.181404
X-RAY DIFFRACTIONf_chiral_restr0.071586
X-RAY DIFFRACTIONf_plane_restr0.005622
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.01970.27851720.23213138331095
2.0197-2.10060.28451740.22313171334597
2.1006-2.19620.23931770.21643247342498
2.1962-2.3120.25261810.213248342998
2.312-2.45680.26421830.21883301348499
2.4568-2.64650.25881830.2193289347299
2.6465-2.91270.25371850.21733326351199
2.9127-3.33410.23021870.208833773564100
3.3341-4.20010.20051890.178634123601100
4.2001-43.30970.19631980.18783583378199

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