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- PDB-3lru: hPRP8 Non-Native Subdomain -

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Basic information

Entry
Database: PDB / ID: 3lru
TitlehPRP8 Non-Native Subdomain
ComponentsPre-mRNA-processing-splicing factor 8
KeywordsRNA BINDING PROTEIN / alternate folding of protein / Disease mutation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / Retinitis pigmentosa / Ribonucleoprotein / RNA-binding / Sensory transduction / Spliceosome / Vision
Function / homology
Function and homology information


U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding ...U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / mRNA splicing, via spliceosome / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / nuclear speck / RNA binding / nucleoplasm / membrane / nucleus
Similarity search - Function
JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core ...JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Pre-mRNA-processing-splicing factor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsSchellenberg, M.J. / Ritchie, D.B. / MacMillan, A.M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Context-dependent remodeling of structure in two large protein fragments.
Authors: Schellenberg, M.J. / Ritchie, D.B. / Wu, T. / Markin, C.J. / Spyracopoulos, L. / MacMillan, A.M.
History
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 27, 2015Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
B: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)36,8812
Polymers36,8812
Non-polymers00
Water4,810267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-52 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.732, 42.176, 98.381
Angle α, β, γ (deg.)90.000, 102.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pre-mRNA-processing-splicing factor 8 / Splicing factor Prp8 / PRP8 homolog / 220 kDa U5 snRNP-specific protein / p220


Mass: 18440.660 Da / Num. of mol.: 2 / Fragment: UNP residues 1831-1990
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRP8, PRPC8, PRPF8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6P2Q9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 12% PEG4000, Tris Ph8, 1,3 diamino-propane, pH 6, vapour diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11586 Å
DetectorDetector: CCD / Date: Jun 27, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11586 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 27.81 / Number: 167934 / Rmerge(I) obs: 0.045 / Χ2: 0.94 / D res high: 2 Å / D res low: 100 Å / Num. obs: 45774 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.3110098.910.0221.3273.8
3.424.3110010.0260.6943.9
2.993.4210010.0330.7773.9
2.712.9910010.050.8353.9
2.522.7110010.0770.9553.8
2.372.5299.810.0940.9263.6
2.252.379910.1140.9413.5
2.152.2598.810.1521.033.4
2.072.1598.410.1910.9463.4
22.0797.710.2751.0313.4
ReflectionResolution: 1.85→100 Å / Num. obs: 30833 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.063 / Χ2: 1.007 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.9270.52930600.98199.8
1.92-1.997.10.37430461.002199.9
1.99-2.087.20.25730451.008199.8
2.08-2.197.40.17631061.0021100
2.19-2.337.40.13430411.0251100
2.33-2.517.50.10130611.0021100
2.51-2.767.50.0830881.0251100
2.76-3.167.50.0530991.0181100
3.16-3.997.40.03731011.0011100
3.99-1006.80.03431861.002199.3

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.6 / FOM acentric: 0.6 / FOM centric: 0.64 / Reflection: 23202 / Reflection acentric: 21705 / Reflection centric: 1497
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-29.1460.910.920.871087896191
3.6-5.70.910.920.8132472928319
2.9-3.60.830.830.7840403757283
2.5-2.90.640.640.5640203794226
2.1-2.50.450.450.4269396616323
2-2.10.270.260.2838693714155

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→29.47 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.211 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.817 / SU B: 3.363 / SU ML: 0.103 / SU R Cruickshank DPI: 0.152 / SU Rfree: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1551 5 %RANDOM
Rwork0.21 ---
obs0.212 30823 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.66 Å2 / Biso mean: 29.79 Å2 / Biso min: 10.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20.12 Å2
2--0.49 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 0 0 267 2708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222490
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.983378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.425104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68315473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9911511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021777
X-RAY DIFFRACTIONr_nbd_refined0.2150.21136
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21707
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2204
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.218
X-RAY DIFFRACTIONr_mcbond_it1.0611.51559
X-RAY DIFFRACTIONr_mcangle_it1.82822461
X-RAY DIFFRACTIONr_scbond_it2.39831060
X-RAY DIFFRACTIONr_scangle_it3.734.5917
LS refinement shellResolution: 1.85→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 110 -
Rwork0.262 2049 -
all-2159 -
obs--95.4 %

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