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- PDB-3e9p: Crystal Structure of Yeast Prp8, Residues 1827-2092 -

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Basic information

Entry
Database: PDB / ID: 3e9p
TitleCrystal Structure of Yeast Prp8, Residues 1827-2092
ComponentsPre-mRNA-splicing factor 8
KeywordsRNA BINDING PROTEIN / SPLICING / nucleotidyl transfer / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding / Spliceosome
Function / homology
Function and homology information


generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / pre-mRNA intronic binding ...generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / mRNA binding / nucleus / cytoplasm
Similarity search - Function
Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / 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 ...Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / 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-splicing factor 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPena, V. / Rozov, A. / Wahl, M.C.
CitationJournal: Embo J. / Year: 2008
Title: Structure and function of an RNase H domain at the heart of the spliceosome.
Authors: Pena, V. / Rozov, A. / Fabrizio, P. / Luhrmann, R. / Wahl, M.C.
History
DepositionAug 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 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-splicing factor 8
B: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)58,5722
Polymers58,5722
Non-polymers00
Water4,666259
1
A: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)29,2861
Polymers29,2861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)29,2861
Polymers29,2861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.117, 84.161, 95.054
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 8


Mass: 29285.818 Da / Num. of mol.: 2 / Fragment: RNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Production host: Escherichia coli (E. coli) / References: UniProt: P33334
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97888 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97888 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 34578 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.18 Å / % possible all: 99.99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.892 / SU B: 14.31 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.263 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29799 1814 5 %RANDOM
Rwork0.23686 ---
all0.307 36392 --
obs0.23991 34578 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.692 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---0.87 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 0 259 4379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224314
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9625866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1315530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24324.439187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1815805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.891524
X-RAY DIFFRACTIONr_chiral_restr0.0790.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023174
X-RAY DIFFRACTIONr_nbd_refined0.2020.22047
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22993
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.212
X-RAY DIFFRACTIONr_mcbond_it0.4791.52706
X-RAY DIFFRACTIONr_mcangle_it0.8524305
X-RAY DIFFRACTIONr_scbond_it1.28231829
X-RAY DIFFRACTIONr_scangle_it1.9354.51561
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 149 -
Rwork0.279 2547 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.034-0.32770.35230.6260.06181.18480.0342-0.03650.0320.08980.0137-0.0120.008-0.0483-0.0479-0.0106-0.00530.0008-0.1077-0.008-0.0602-37.699-2.71610.575
22.6431-0.85630.3364.0834-0.98651.0411-0.03570.1151-0.0378-0.21550.0764-0.29220.10210.0866-0.0407-0.0362-0.00170.0448-0.1002-0.0323-0.0498-29.921-11.602-8.281
31.29650.3686-0.81892.2605-0.58591.1333-0.0437-0.0120.0468-0.11540.00360.170.01650.04680.0401-0.04-0.0013-0.0257-0.13460.0214-0.0665-26.367-23.81624.674
41.650.3670.15762.5608-0.3571.5589-0.0388-0.1839-0.0896-0.03640.0487-0.29310.11670.0757-0.0099-0.1190.0430.0209-0.06370.09470.011-6.427-33.49328.735
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1833 - 19931 - 161
2X-RAY DIFFRACTION2AA1994 - 2087162 - 255
3X-RAY DIFFRACTION3BB1833 - 19931 - 161
4X-RAY DIFFRACTION4BB1994 - 2087162 - 255

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