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- PDB-3sbs: Crystal structure of Aar2 protein -

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Basic information

Entry
Database: PDB / ID: 3sbs
TitleCrystal structure of Aar2 protein
ComponentsA1 cistron-splicing factor AAR2
KeywordsSPLICING / VHS like domain
Function / homology
Function and homology information


spliceosomal tri-snRNP complex assembly / U5 snRNP / spliceosomal snRNP assembly / cytoplasm
Similarity search - Function
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 ...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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
A1 cistron-splicing factor AAR2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.0Apr 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

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Assembly

Deposited unit
A: A1 cistron-splicing factor AAR2


Theoretical massNumber of molelcules
Total (without water)42,8061
Polymers42,8061
Non-polymers00
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.772, 101.772, 119.749
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: 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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.62 Å3/Da / Density % sol: 66.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5
Details: 0.1 M sodium acetate, pH 5.0, 2.0 M sodium formate, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 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: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→77.5 Å / Num. all: 37326 / Num. obs: 37260 / % possible obs: 99.9 % / Observed criterion σ(I): 12.3
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.79 / % 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: 2.1→29.937 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 1862 5 %RANDOM
Rwork0.165 ---
obs0.1667 37260 99.84 %-
all-37326 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.833 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.307 Å2-0 Å20 Å2
2---4.307 Å2-0 Å2
3---8.6139 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 0 315 2813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012805
X-RAY DIFFRACTIONf_angle_d1.1883815
X-RAY DIFFRACTIONf_dihedral_angle_d14.5861066
X-RAY DIFFRACTIONf_chiral_restr0.092389
X-RAY DIFFRACTIONf_plane_restr0.004506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.1570.26111260.24312689X-RAY DIFFRACTION100
2.157-2.22040.26541260.21682684X-RAY DIFFRACTION100
2.2204-2.29210.24211480.20532682X-RAY DIFFRACTION100
2.2921-2.3740.25781300.19792693X-RAY DIFFRACTION100
2.374-2.4690.23161480.18222680X-RAY DIFFRACTION100
2.469-2.58130.22311340.17432705X-RAY DIFFRACTION100
2.5813-2.71730.22211410.17952712X-RAY DIFFRACTION100
2.7173-2.88740.22731530.17612696X-RAY DIFFRACTION100
2.8874-3.11010.22121680.17682695X-RAY DIFFRACTION100
3.1101-3.42270.2051570.17282723X-RAY DIFFRACTION100
3.4227-3.9170.17731520.15092741X-RAY DIFFRACTION100
3.917-4.93150.15771320.12532802X-RAY DIFFRACTION100
4.9315-29.94030.17821470.15862896X-RAY DIFFRACTION98
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)
12.7247-1.4626-0.86251.85211.33081.41280.0343-0.16090.07350.07590.0068-0.07230.132-0.0434-0.02970.1162-0.03760.00750.1783-0.00640.145211.8857-35.9159-17.6042
22.4879-1.129-0.44032.18440.25660.58710.11550.0868-0.0817-0.0946-0.13990.1328-0.0037-0.07380.02620.1737-0.02080.01310.3078-0.05650.2005-12.2907-23.5558-15.205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 1:154
2X-RAY DIFFRACTION2chain A and resseq 173:318

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