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- PDB-3sbg: Crystal structure of a Prp8 C-terminal fragment -

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Basic information

Entry
Database: PDB / ID: 3sbg
TitleCrystal structure of a Prp8 C-terminal fragment
ComponentsPre-mRNA-splicing factor 8
KeywordsSPLICING / Prp8p / RNaseH domain / Jab1/MPN domain
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 / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain ...Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 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 / 3-Layer(aba) 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: 3.28 Å
AuthorsWeber, G. / Santos, K. / Holton, N. / Wahl, M.C.
CitationJournal: Genes Dev. / Year: 2011
Title: Mechanism for Aar2p function as a U5 snRNP assembly factor.
Authors: Weber, G. / Cristao, V.F. / de L Alves, F. / Santos, K.F. / Holton, N. / Rappsilber, J. / Beggs, J.D. / Wahl, M.C.
History
DepositionJun 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)64,0301
Polymers64,0301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)145.786, 73.598, 72.882
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pre-mRNA-splicing factor 8


Mass: 64029.832 Da / Num. of mol.: 1 / Fragment: Yeast Prp8p C-terminal domain, 1836-2397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: DBF3, DNA39, PRP8, RNA8, SLT21, USA2, YHR165C / Production host: Escherichia coli (E. coli) / References: UniProt: P33334

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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: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 M ammonium tartrate, 5 mM NiCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9814 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 29, 2010
RadiationMonochromator: Double crystal (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 3.28→30 Å / Num. all: 11839 / Num. obs: 11830 / % possible obs: 99.6 % / Observed criterion σ(F): 5.6 / Observed criterion σ(I): 5.6
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1178 / Rsym value: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.28→27.077 Å / SU ML: 0.47 / σ(F): 1.35 / Phase error: 26.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 585 4.95 %RANDOM
Rwork0.2188 ---
all0.221 11839 --
obs0.221 11830 98.79 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 9.432 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3514 Å2-0 Å23.8244 Å2
2--6.159 Å20 Å2
3----10.5104 Å2
Refinement stepCycle: LAST / Resolution: 3.28→27.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 0 0 3983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024070
X-RAY DIFFRACTIONf_angle_d0.6235521
X-RAY DIFFRACTIONf_dihedral_angle_d14.9721500
X-RAY DIFFRACTIONf_chiral_restr0.05632
X-RAY DIFFRACTIONf_plane_restr0.002697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.60890.33081360.27662722X-RAY DIFFRACTION97
3.6089-4.12950.27331480.22022828X-RAY DIFFRACTION100
4.1295-5.19680.23611510.19182851X-RAY DIFFRACTION100
5.1968-27.0780.24741500.20892844X-RAY DIFFRACTION99
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)
11.51290.0046-0.00671.2546-0.81773.1953-0.02060.2225-0.0628-0.07590.07420.0510.02140.01730.0020.0623-0.0193-0.0340.0664-0.04530.0416-29.607622.2748-54.3227
22.49970.6861-0.23542.0358-0.29982.46320.0683-0.06-0.0557-0.1029-0.0371-0.06620.2423-0.0056-0.00060.04990.00050.00010.0417-0.01720.0967-14.49131.9413-22.0015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A and resid 1833:2086
2X-RAY DIFFRACTION2Chain A and resid 2148:2390

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