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- PDB-3e9o: Crystal Structure of Yeast Prp8, Residues 1836-2092 -

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Basic information

Entry
Database: PDB / ID: 3e9o
TitleCrystal Structure of Yeast Prp8, Residues 1836-2092
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 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding ...generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / 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 / MAD / Resolution: 2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)29,8691
Polymers29,8691
Non-polymers00
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.857, 46.857, 102.995
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Pre-mRNA-splicing factor 8


Mass: 29869.074 Da / Num. of mol.: 1 / 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


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
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: BESSY / Beamline: 14.2 / Wavelength: 0.97968, 0.97987, 0.91841
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 28, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979681
20.979871
30.918411
ReflectionResolution: 2→50 Å / Num. all: 33148 / Num. obs: 17446 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.9 / SU B: 8.395 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.216 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24515 861 5.1 %RANDOM
Rwork0.17676 ---
all0.32 16963 --
obs0.18011 16102 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.425 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 0 269 2320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222155
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9612932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2195268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05124.67492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12215404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4011511
X-RAY DIFFRACTIONr_chiral_restr0.0720.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021589
X-RAY DIFFRACTIONr_nbd_refined0.1940.21044
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21515
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.224
X-RAY DIFFRACTIONr_mcbond_it0.4971.51362
X-RAY DIFFRACTIONr_mcangle_it0.86822164
X-RAY DIFFRACTIONr_scbond_it1.6983907
X-RAY DIFFRACTIONr_scangle_it2.5884.5768
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 74 -
Rwork0.234 1101 -
obs--93.11 %
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)
11.1419-0.16230.38841.2093-0.28370.78950.01390.08310.0484-0.0123-0.0033-0.05110.05740.1019-0.0106-0.080.02560.0055-0.02720.00740.0149-23.75760.213-28.682
21.07860.4627-0.62330.97320.21651.8882-0.0458-0.0088-0.0480.02680.0336-0.0186-0.0718-0.05290.0122-0.08770.0261-0.0057-0.03340.02180.0347-46.64961.86-25.285
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1833 - 19934 - 164
2X-RAY DIFFRACTION2AA1994 - 2087165 - 258

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