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- PDB-4rz9: Pre-mRNA-splicing factor 38A AS 1-179 -

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Basic information

Entry
Database: PDB / ID: 4rz9
TitlePre-mRNA-splicing factor 38A AS 1-179
ComponentsPre-mRNA-splicing factor 38A
KeywordsRNA BINDING PROTEIN / RNA-splicing
Function / homology
Function and homology information


U2-type precatalytic spliceosome / precatalytic spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Pre-mRNA-splicing factor 38, C-terminal / Pre-mRNA-splicing factor 38-associated hydrophilic C-term / Pre-mRNA-splicing factor 38 / PRP38 family
Similarity search - Domain/homology
Pre-mRNA-splicing factor 38A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.28 Å
AuthorsSchuetze, T. / Weber, G. / Wahl, M.C.
CitationJournal: To be Published
Title: The N-terminal domain of the unusual SR protein hPrp38 is an interaction hub in the spliceosome
Authors: Schuetze, T. / Apelt, L. / Ulrich, A. / Weber, G. / Bartlick, N. / Stelzl, U. / Wahl, M.C.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor 38A


Theoretical massNumber of molelcules
Total (without water)21,1621
Polymers21,1621
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.886, 61.848, 67.710
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-splicing factor 38A


Mass: 21161.561 Da / Num. of mol.: 1 / Fragment: UNP residues 27-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPF38A / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q8NAV1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, and 15% (w/v) PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.28→19.04 Å / Num. all: 46138 / Num. obs: 46008 / Rmerge(I) obs: 0.055

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.28→19.04 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 13.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1502 2318 5.04 %
Rwork0.1264 --
obs0.1276 46008 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.28→19.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 0 247 1731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111806
X-RAY DIFFRACTIONf_angle_d1.3542499
X-RAY DIFFRACTIONf_dihedral_angle_d14.185781
X-RAY DIFFRACTIONf_chiral_restr0.084277
X-RAY DIFFRACTIONf_plane_restr0.006329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.30610.20411460.19522531X-RAY DIFFRACTION100
1.3061-1.33450.24441300.17842540X-RAY DIFFRACTION100
1.3345-1.36560.20041390.17332527X-RAY DIFFRACTION100
1.3656-1.39970.2011490.16132528X-RAY DIFFRACTION100
1.3997-1.43750.16091270.1442546X-RAY DIFFRACTION100
1.4375-1.47980.16121360.1322526X-RAY DIFFRACTION100
1.4798-1.52760.14921350.12342548X-RAY DIFFRACTION100
1.5276-1.58210.14921260.11192560X-RAY DIFFRACTION100
1.5821-1.64540.15281350.10162534X-RAY DIFFRACTION100
1.6454-1.72030.14631320.10252574X-RAY DIFFRACTION100
1.7203-1.81090.13911320.10492567X-RAY DIFFRACTION100
1.8109-1.92430.13181360.10552564X-RAY DIFFRACTION100
1.9243-2.07270.13271390.10142595X-RAY DIFFRACTION100
2.0727-2.28090.15051330.10352584X-RAY DIFFRACTION100
2.2809-2.61030.12981390.11512603X-RAY DIFFRACTION100
2.6103-3.28590.13011370.13292639X-RAY DIFFRACTION100
3.2859-19.040.15941470.14352724X-RAY DIFFRACTION99

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