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- PDB-3enb: Crystal Structure of PRP8 core domain IV -

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Basic information

Entry
Database: PDB / ID: 3enb
TitleCrystal Structure of PRP8 core domain IV
ComponentsPre-mRNA-processing-splicing factor 8
KeywordsRNA BINDING PROTEIN / PRP8 domain IV / beta finger / RNase H / spliceosome / U5-220K / Disease mutation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / Retinitis pigmentosa / RNA-binding / Sensory transduction / 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 splicing, via spliceosome / mRNA processing / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / nuclear speck / RNA binding / nucleoplasm / membrane / nucleus
Similarity search - Function
Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / 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 ...Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / 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. / Nucleotidyltransferase; domain 5 / Ribonuclease H-like superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pre-mRNA-processing-splicing factor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsSchellenberg, M.J. / Ritchie, D.B. / MacMillan, A.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural elucidation of a PRP8 core domain from the heart of the spliceosome.
Authors: Ritchie, D.B. / Schellenberg, M.J. / Gesner, E.M. / Raithatha, S.A. / Stuart, D.T. / Macmillan, A.M.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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

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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)51,0782
Polymers51,0782
Non-polymers00
Water6,828379
1
A: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)25,5391
Polymers25,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)25,5391
Polymers25,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.397, 78.062, 93.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 25538.787 Da / Num. of mol.: 2 / Fragment: UNP residues 1769-1990
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPF8, PRPC8 / Plasmid: pMALC2X / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6P2Q9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5 M NaCl, 100 mM Tris-HCl pH 7.0, 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872, 0.9796, 1.0200, 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2006
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.1158721
20.97961
31.021
40.97971
ReflectionRedundancy: 2.9 % / Av σ(I) over netI: 27.88 / Number: 138717 / Rmerge(I) obs: 0.051 / Χ2: 1.01 / D res high: 2.3 Å / D res low: 100 Å / Num. obs: 47374 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.961009810.0281.0192.9
3.934.9699.510.031.0363
3.443.9399.710.0380.983
3.123.4499.610.051.0073
2.93.1299.610.0721.0353
2.732.999.510.0961.053
2.592.7399.210.1361.0183
2.482.599910.1870.9792.9
2.382.4898.610.2240.9642.9
2.32.389810.2640.9812.8
ReflectionResolution: 1.85→100 Å / Num. obs: 47833 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.044 / Χ2: 1.023 / Net I/σ(I): 27.879
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.923.50.40846871.186199.6
1.92-1.993.90.29247401.121199.8
1.99-2.0840.19947001.062199.8
2.08-2.194.10.12347360.9931100
2.19-2.3340.11247321.017199.7
2.33-2.514.10.06747910.9441100
2.51-2.764.10.05347680.9471100
2.76-3.164.10.03748220.9631100
3.16-3.9940.02948431.045199.8
3.99-1003.80.02150140.994198.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.36 Å / D res low: 30 Å / FOM : 0.47 / Reflection: 23362
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97963.85-8.32
13 wavelength21.020.54-2.84
13 wavelength30.97970.5-8.05
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se14.6310.8010.240.2160.629
2Se600.140.4940.1350.837
3Se600.160.5820.1860.761
4Se41.4410.1010.3240.030.711
Phasing MAD shell
Resolution (Å)FOM Reflection
8.39-300.691192
5.33-8.390.661961
4.18-5.330.582503
3.54-4.180.542884
3.13-3.540.513266
2.84-3.130.453565
2.61-2.840.383843
2.43-2.610.284148

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 1.85→59.98 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.294 / WRfactor Rwork: 0.242 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.854 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2414 5.1 %RANDOM
Rwork0.206 ---
obs0.208 47768 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.75 Å2 / Biso mean: 27.164 Å2 / Biso min: 12.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.85→59.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 0 379 3818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223520
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9634787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1625419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37124.564149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54515648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8051516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022554
X-RAY DIFFRACTIONr_nbd_refined0.20.21637
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2304
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.225
X-RAY DIFFRACTIONr_mcbond_it0.8761.52184
X-RAY DIFFRACTIONr_mcangle_it1.46423470
X-RAY DIFFRACTIONr_scbond_it2.13831534
X-RAY DIFFRACTIONr_scangle_it3.3344.51317
LS refinement shellResolution: 1.85→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 175 -
Rwork0.242 3013 -
all-3188 -
obs--97.03 %
Refinement TLS params.Method: refined / Origin x: 49.68 Å / Origin y: 2.484 Å / Origin z: 17.129 Å
111213212223313233
T0.3102 Å20.0043 Å20.0033 Å2-0.306 Å20.0008 Å2--0.3036 Å2
L0.1663 °20.079 °20.0273 °2-0.1702 °20.016 °2--0.1467 °2
S0.0034 Å °-0.0116 Å °-0.0001 Å °0.0063 Å °-0.0021 Å °0.0166 Å °0.0044 Å °-0.0164 Å °-0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1774 - 1988
2X-RAY DIFFRACTION1A1771 - 1989

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