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- PDB-4lk2: Crystal structure of RNA splicing effector Prp5 -

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Basic information

Entry
Database: PDB / ID: 4lk2
TitleCrystal structure of RNA splicing effector Prp5
ComponentsPre-mRNA-processing ATP-dependent RNA helicase PRP5
KeywordsHYDROLASE / Prp5 / DEAD box family / RNA splicing
Function / homology
Function and homology information


mRNA branch site recognition / ATP-dependent activity, acting on RNA / commitment complex / mRNA splicing, via spliceosome / RNA helicase activity / nucleic acid binding / RNA helicase / ATP hydrolysis activity / ATP binding / nucleus
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
NICKEL (II) ION / Pre-mRNA-processing ATP-dependent RNA helicase PRP5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 / Category: citation / citation_author
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
Revision 1.2Mar 20, 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,2703
Polymers110,2112
Non-polymers591
Water4,270237
1
A: Pre-mRNA-processing ATP-dependent RNA helicase PRP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1642
Polymers55,1051
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pre-mRNA-processing ATP-dependent RNA helicase PRP5


Theoretical massNumber of molelcules
Total (without water)55,1051
Polymers55,1051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.159, 86.081, 127.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 55105.434 Da / Num. of mol.: 2 / 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-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris propane, 20% PEG 3350, 0.2M NaF , 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
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 59417

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→38.881 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.7773 / SU ML: 0.25 / σ(F): 0 / Phase error: 28.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 1748 3.39 %
Rwork0.2116 --
obs0.2131 51501 93.13 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.57 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 94.05 Å2 / Biso mean: 43.1314 Å2 / Biso min: 17.94 Å2
Baniso -1Baniso -2Baniso -3
1--5.2973 Å20 Å2-0 Å2
2--21.9365 Å20 Å2
3----16.6392 Å2
Refinement stepCycle: LAST / Resolution: 2.12→38.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6733 0 1 237 6971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086878
X-RAY DIFFRACTIONf_angle_d1.0869298
X-RAY DIFFRACTIONf_dihedral_angle_d14.8472585
X-RAY DIFFRACTIONf_chiral_restr0.0731116
X-RAY DIFFRACTIONf_plane_restr0.0041184
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 (%)
2.12-2.19580.30861660.26214545471187
2.1958-2.28370.30381640.24474689485389
2.2837-2.38760.34151710.24424837500891
2.3876-2.51350.32631790.24314940511994
2.5135-2.67090.3481740.24125008518294
2.6709-2.87710.2981780.22995007518595
2.8771-3.16650.26761740.21555143531796
3.1665-3.62440.24391790.20535174535396
3.6244-4.56520.22191840.18295161534595
4.5652-38.88730.19471790.19855249542893

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