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- PDB-3sbt: Crystal structure of a Aar2-Prp8 complex -

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Basic information

Entry
Database: PDB / ID: 3sbt
TitleCrystal structure of a Aar2-Prp8 complex
Components
  • A1 cistron-splicing factor AAR2
  • Pre-mRNA-splicing factor 8
KeywordsSPLICING / RNaseH like domain / VHS like domain / U5 snRNP assembly
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 / Aar2, C-terminal domain-like / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / AAR2 N-terminal domain / A1 cistron-splicing factor, AAR2 / AAR2, N-terminal / AAR2, C-terminal ...Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / Aar2, C-terminal domain-like / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / 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 / Nucleotidyltransferase; domain 5 / Ribonuclease H-like superfamily / Up-down Bundle / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / 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: 1.799 Å
AuthorsWeber, G. / Santos, K.F. / 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 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references
Revision 1.2Feb 20, 2013Group: Derived calculations
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Pre-mRNA-splicing factor 8
B: A1 cistron-splicing factor AAR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7595
Polymers72,4912
Non-polymers2683
Water10,539585
1
B: A1 cistron-splicing factor AAR2

A: Pre-mRNA-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7595
Polymers72,4912
Non-polymers2683
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
2
A: Pre-mRNA-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9544
Polymers29,6851
Non-polymers2683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: A1 cistron-splicing factor AAR2


Theoretical massNumber of molelcules
Total (without water)42,8061
Polymers42,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.334, 82.019, 94.057
Angle α, β, γ (deg.)90.00, 108.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pre-mRNA-splicing factor 8


Mass: 29685.305 Da / Num. of mol.: 1
Fragment: Yeast Prp8p RNaseH like domain, residues 1836-2092
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 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2 / References: UniProt: P33334
#2: Protein A1 cistron-splicing factor AAR2


Mass: 42805.824 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, YBL06.06, YBL0611, YBL074C / Plasmid: pETM-13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2 / References: UniProt: P32357
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.1 M lithium sulfate, 20 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9814 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 19, 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: 1.799→89.1 Å / Num. all: 59465 / Num. obs: 59439 / % possible obs: 99.6 % / Observed criterion σ(I): 26.4 / Rsym value: 0.03
Reflection shellResolution: 1.8→1.83 Å / Rsym value: 0.44 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_353)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.799→26.735 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 2999 5.05 %RANDOM
Rwork0.1619 ---
all0.1653 59465 --
obs0.1637 59439 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.428 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.1844 Å2-0 Å2-0.7724 Å2
2---6.7593 Å20 Å2
3----2.4251 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.799→26.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4539 0 15 585 5139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014845
X-RAY DIFFRACTIONf_angle_d1.1976585
X-RAY DIFFRACTIONf_dihedral_angle_d13.5871814
X-RAY DIFFRACTIONf_chiral_restr0.09721
X-RAY DIFFRACTIONf_plane_restr0.005846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7994-1.82890.26091390.22182601X-RAY DIFFRACTION97
1.8289-1.86040.23511280.21272705X-RAY DIFFRACTION100
1.8604-1.89420.24721460.20252678X-RAY DIFFRACTION99
1.8942-1.93060.28181530.20272639X-RAY DIFFRACTION99
1.9306-1.970.22631330.18572674X-RAY DIFFRACTION100
1.97-2.01280.24451360.17842730X-RAY DIFFRACTION100
2.0128-2.05970.20651340.17512651X-RAY DIFFRACTION100
2.0597-2.11110.25021520.17342693X-RAY DIFFRACTION100
2.1111-2.16820.22011390.16432696X-RAY DIFFRACTION100
2.1682-2.2320.2061280.15522697X-RAY DIFFRACTION100
2.232-2.3040.20691300.15982680X-RAY DIFFRACTION100
2.304-2.38630.18271380.15962699X-RAY DIFFRACTION100
2.3863-2.48170.23241380.16632714X-RAY DIFFRACTION100
2.4817-2.59460.20391440.16252688X-RAY DIFFRACTION100
2.5946-2.73130.22881450.17312688X-RAY DIFFRACTION100
2.7313-2.90220.22081360.17212701X-RAY DIFFRACTION100
2.9022-3.1260.2121600.17442675X-RAY DIFFRACTION100
3.126-3.440.18461590.15322693X-RAY DIFFRACTION100
3.44-3.93640.16281490.13042700X-RAY DIFFRACTION100
3.9364-4.95430.14561480.12622715X-RAY DIFFRACTION100
4.9543-26.73820.18041640.1682723X-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)
11.3346-0.0799-0.12221.61650.34611.40690.0140.0443-0.0426-0.1256-0.0359-0.05750.0122-0.05420.01680.1501-0.00740.02450.15070.03730.14264.75497.1725-18.477
20.8143-0.4978-0.32882.31030.26671.40480.2206-0.11290.3205-0.1134-0.0824-0.6319-0.27590.3491-0.10180.1149-0.05280.0320.17060.02270.297820.025522.8698-10.4268
31.83180.45010.3022.62890.62242.35720.0437-0.06770.03060.1877-0.0468-0.15430.05380.20260.01460.1450.0108-0.01520.17960.05990.189149.94417.9389-17.3613
40.732-0.13570.67221.3983-0.71353.3663-0.01810.10580.0632-0.15510.01170.16040.261-0.0238-0.01340.1420.0172-0.01180.13220.02140.11635.2089-0.8556-38.1081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A and resseq 1834:1991
2X-RAY DIFFRACTION2Chain A and resseq 1992:2086
3X-RAY DIFFRACTION3Chain B and resseq 1:153
4X-RAY DIFFRACTION4Chain B and resseq 171:317

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