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- PDB-3zef: Crystal structure of Prp8:Aar2 complex: second crystal form at 3.... -

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Basic information

Entry
Database: PDB / ID: 3zef
TitleCrystal structure of Prp8:Aar2 complex: second crystal form at 3.1 Angstrom resolution
Components
  • A1 CISTRON-SPLICING FACTOR AAR2
  • PRE-MRNA-SPLICING FACTOR 8
KeywordsTRANSLATION / PRE-MRNA SPLICING / SPLICEOSOME / U5 SNRNP
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 / Prp19 complex / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / 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 / Prp19 complex / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / spliceosomal snRNP assembly / 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
Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain / Pre-mRNA-processing-splicing factor 8 (Prp8), endonuclease domain / tt1808, chain A / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Cytidine Deaminase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Cytidine Deaminase; domain 2 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Aar2, C-terminal domain-like / A1 cistron-splicing factor, AAR2 ...Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain / Pre-mRNA-processing-splicing factor 8 (Prp8), endonuclease domain / tt1808, chain A / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Cytidine Deaminase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Cytidine Deaminase; domain 2 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Aar2, C-terminal domain-like / A1 cistron-splicing factor, AAR2 / AAR2, N-terminal / AAR2, C-terminal / AAR2, C-terminal domain superfamily / AAR2, N-terminal domain superfamily / AAR2 C-terminal repeat region / AAR2 N-terminal domain / 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. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Ribonuclease H-like superfamily / Alpha-Beta Complex / Sandwich / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
A1 cistron-splicing factor AAR2 / Pre-mRNA-splicing factor 8
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGalej, W.P. / Oubridge, C. / Newman, A.J. / Nagai, K.
CitationJournal: Nature / Year: 2013
Title: Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome
Authors: Galej, W.P. / Oubridge, C. / Newman, A.J. / Nagai, K.
History
DepositionDec 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Feb 27, 2013Group: Structure summary
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A1 CISTRON-SPLICING FACTOR AAR2
B: PRE-MRNA-SPLICING FACTOR 8
D: A1 CISTRON-SPLICING FACTOR AAR2
E: PRE-MRNA-SPLICING FACTOR 8


Theoretical massNumber of molelcules
Total (without water)436,7344
Polymers436,7344
Non-polymers00
Water00
1
A: A1 CISTRON-SPLICING FACTOR AAR2
B: PRE-MRNA-SPLICING FACTOR 8


Theoretical massNumber of molelcules
Total (without water)218,3672
Polymers218,3672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-26.9 kcal/mol
Surface area78560 Å2
MethodPISA
2
D: A1 CISTRON-SPLICING FACTOR AAR2
E: PRE-MRNA-SPLICING FACTOR 8


Theoretical massNumber of molelcules
Total (without water)218,3672
Polymers218,3672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-24.5 kcal/mol
Surface area79400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.420, 177.841, 216.601
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 A1 CISTRON-SPLICING FACTOR AAR2 / AAR2


Mass: 41734.688 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PRS424 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: P32357
#2: Protein PRE-MRNA-SPLICING FACTOR 8 / PRP8


Mass: 176632.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PRS426 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: P33334
Sequence detailsTHE DEPOSITED SEQUENCE REPRESENTS RESIDUES 885-2414 OF THE GENBANK DATABASE ENTRY WITH MUTATIONS ...THE DEPOSITED SEQUENCE REPRESENTS RESIDUES 885-2414 OF THE GENBANK DATABASE ENTRY WITH MUTATIONS LEU1961ASN AND ILE1999LEU

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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: 2.75 Å3/Da / Density % sol: 0.55 %
Description: 3SBT SEPARATED INTO SINGLE CHAINS FOR MR SEARCH
Crystal growpH: 7.9
Details: 7-9% PEG 8000, 100 MM NA-CITRATE PH 7.9, 50-200 MM AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→137.5 Å / Num. obs: 97506 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.4
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0016refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHASERphasing
SHELXEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3SBT, 2OG4

3sbt

2og4


Resolution: 3.1→137.45 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.886 / SU B: 25.665 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.489 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26711 4442 5 %RANDOM
Rwork0.22022 ---
obs0.22253 84013 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.693 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å20 Å2
2--6.95 Å20 Å2
3----4.67 Å2
Refinement stepCycle: LAST / Resolution: 3.1→137.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28285 0 0 0 28285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01928965
X-RAY DIFFRACTIONr_bond_other_d0.0060.0227431
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9539250
X-RAY DIFFRACTIONr_angle_other_deg1.042363077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37153439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44124.1911415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.135155097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.43515169
X-RAY DIFFRACTIONr_chiral_restr0.0810.24305
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02132438
X-RAY DIFFRACTIONr_gen_planes_other0.0040.026875
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.1189.48413825
X-RAY DIFFRACTIONr_mcbond_other6.1179.48413824
X-RAY DIFFRACTIONr_mcangle_it9.8414.2117241
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6679.77315140
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 317 -
Rwork0.336 6135 -
obs--99.94 %

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