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- PDB-4ilg: Crystal structure of Aar2p in complex with the Prp8p RNaseH and J... -

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Basic information

Entry
Database: PDB / ID: 4ilg
TitleCrystal structure of Aar2p in complex with the Prp8p RNaseH and Jab1/MPN domains
Components
  • (Pre-mRNA-splicing factor 8) x 2
  • A1 cistron-splicing factor AAR2
KeywordsSPLICING / U5 snRNP assembly / Aar2 / Prp8
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
Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Cytidine Deaminase, 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 ...Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Cytidine Deaminase, 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 / Nucleotidyltransferase; domain 5 / Alpha Horseshoe / Ribonuclease H-like superfamily / Up-down Bundle / 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: 2.1 Å
AuthorsWeber, G. / Heroven, A.C. / Santos, K.F. / Wahl, M.C.
CitationJournal: Genes Dev. / Year: 2013
Title: Structural basis for dual roles of Aar2p in U5 snRNP assembly.
Authors: Weber, G. / Cristao, V.F. / Santos, K.F. / Jovin, S.M. / Heroven, A.C. / Holton, N. / Luhrmann, R. / Beggs, J.D. / Wahl, M.C.
History
DepositionDec 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Structure summary
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Pre-mRNA-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4504
Polymers100,2113
Non-polymers2381
Water12,412689
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-24 kcal/mol
Surface area39020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.768, 63.739, 110.518
Angle α, β, γ (deg.)90.00, 95.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein A1 cistron-splicing factor AAR2


Mass: 40219.867 Da / Num. of mol.: 1 / Mutation: Residues 153-170 replaced by 5 Serines
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P32357
#2: Protein Pre-mRNA-splicing factor 8


Mass: 29501.113 Da / Num. of mol.: 1 / Fragment: yPrp8 RNaseH (UNP Residues 1835-2090)
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P33334
#3: Protein Pre-mRNA-splicing factor 8


Mass: 30490.338 Da / Num. of mol.: 1 / Fragment: yPrp8 Jab1/MPN (UNP Residues 2147-2413)
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P33334
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES-NaOH, pH 7.5, 12 % (w/v) PEG 6000 and 0.6 M KCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 30, 2011
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→34.3 Å / Num. all: 68910 / Num. obs: 68679 / % possible obs: 99.9 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6 / Redundancy: 3.4 % / Rmerge(I) obs: 0.207 / Rsym value: 0.09 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.15 Å / % possible obs: 99.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 1.154 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.861

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SBT, 2OG4

3sbt

2og4


Resolution: 2.1→31.869 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 3063 4.46 %
Rwork0.1803 --
obs0.1823 68667 99.69 %
all-68910 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.555 Å2 / ksol: 0.291 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8921 Å20 Å2-7.2863 Å2
2---3.6202 Å2-0 Å2
3---4.5123 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6653 0 15 689 7357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017019
X-RAY DIFFRACTIONf_angle_d1.1819536
X-RAY DIFFRACTIONf_dihedral_angle_d14.712635
X-RAY DIFFRACTIONf_chiral_restr0.0821039
X-RAY DIFFRACTIONf_plane_restr0.0051225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13280.34621390.29322991X-RAY DIFFRACTION100
2.1328-2.16780.29411380.26852977X-RAY DIFFRACTION100
2.1678-2.20510.30681400.24972955X-RAY DIFFRACTION100
2.2051-2.24520.28621480.25082938X-RAY DIFFRACTION100
2.2452-2.28840.40531140.36052937X-RAY DIFFRACTION98
2.2884-2.33510.33461230.25492973X-RAY DIFFRACTION100
2.3351-2.38590.29921640.21632940X-RAY DIFFRACTION100
2.3859-2.44130.24051390.20782968X-RAY DIFFRACTION100
2.4413-2.50240.24291470.19932988X-RAY DIFFRACTION100
2.5024-2.570.30051350.20512965X-RAY DIFFRACTION100
2.57-2.64560.25161340.18353006X-RAY DIFFRACTION100
2.6456-2.73090.23491370.18912962X-RAY DIFFRACTION100
2.7309-2.82850.26841500.19212964X-RAY DIFFRACTION100
2.8285-2.94170.26361380.19092984X-RAY DIFFRACTION100
2.9417-3.07540.24991360.18052967X-RAY DIFFRACTION100
3.0754-3.23740.21961380.17173020X-RAY DIFFRACTION100
3.2374-3.440.21321400.16612957X-RAY DIFFRACTION100
3.44-3.70530.19711380.16022993X-RAY DIFFRACTION99
3.7053-4.07750.15881360.14263007X-RAY DIFFRACTION100
4.0775-4.66590.19621410.13052992X-RAY DIFFRACTION100
4.6659-5.87250.18421410.14653037X-RAY DIFFRACTION99
5.8725-31.87320.18011470.15633083X-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)
10.56180.29580.72320.85980.56681.1152-0.10.24840.0064-0.57120.11620.10710.00220.1006-0.11770.5094-0.056-0.21450.1122-0.05370.0619-27.2562-26.6528-46.0088
21.10070.20740.38382.2362-0.08950.7303-0.02120.0906-0.0011-0.1270.0559-0.16020.00610.1254-0.00830.06870.0289-0.00780.0665-0.03210.1018-9.666.6454-19.4523
32.3685-0.6765-0.00242.15310.28181.7175-0.02840.27860.02780.0384-0.0324-0.3492-0.01160.3683-0.07-0.01270.04880.03440.3188-0.0350.16428.180811.8386-8.6863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain B and resid 1834:2085
3X-RAY DIFFRACTION3chain C and resid 2148:2392

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