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- PDB-4i43: Crystal structure of Prp8:Aar2 complex -

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Basic information

Entry
Database: PDB / ID: 4i43
TitleCrystal structure of Prp8:Aar2 complex
Components
  • A1 cistron-splicing factor AAR2
  • Pre-mRNA-splicing factor 8
KeywordsSPLICING / spliceosome / U5 snRNP / Prp8 / Reverse Transcriptase / Aar2 / Endonuclease / RNase H / Jab1/MPN / pre-mRNA splicing
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
Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain / Pre-mRNA-processing-splicing factor 8 (Prp8), endonuclease domain / tt1808, chain A / Cytidine Deaminase, domain 2 / Aar2, C-terminal domain-like / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Cytidine Deaminase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / AAR2 N-terminal domain ...Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain / Pre-mRNA-processing-splicing factor 8 (Prp8), endonuclease domain / tt1808, chain A / Cytidine Deaminase, domain 2 / Aar2, C-terminal domain-like / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Cytidine Deaminase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / AAR2 N-terminal domain / 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 / 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: 2 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
DepositionNov 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: A1 cistron-splicing factor AAR2
B: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)225,1852
Polymers225,1852
Non-polymers00
Water12,070670
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-29 kcal/mol
Surface area78550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.856, 158.595, 220.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

21B-2758-

HOH

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Components

#1: Protein A1 cistron-splicing factor AAR2


Mass: 44967.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: AAR2, YBL074C, YBL06.06, YBL0611 / Plasmid: modified pRS424 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: P32357
#2: Protein Pre-mRNA-splicing factor 8


Mass: 180217.641 Da / Num. of mol.: 1 / Fragment: UNP residues 885-2413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Plasmid: modified pRS426 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: P33334
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 293 K / pH: 7.9
Details: 7-9% PEG8000 0.1M sodium citrate 0.05-0.15M ammonium sulfate , pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2012
RadiationMonochromator: SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2→48.3 Å / Num. obs: 139972 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 5 % / Rmerge(I) obs: 0.0126 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHASERphasing
SHELXEmodel building
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SBT, 2OG4

3sbt

2og4


Resolution: 2→48.3 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.165 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 7046 5 %RANDOM
Rwork0.198 ---
obs0.201 139972 100 %-
all-140035 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.52 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å2-0 Å20 Å2
2--2 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14232 0 0 670 14902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01914573
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213766
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.9519744
X-RAY DIFFRACTIONr_angle_other_deg0.576331669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.76151728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15824.268717
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.103152565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.331584
X-RAY DIFFRACTIONr_chiral_restr0.0650.22160
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02116324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023450
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 514 -
Rwork0.294 9770 -
obs--100 %

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