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- PDB-4ili: Crystal structure of an Aar2p S253E phosphomimetic mutant protein -

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Basic information

Entry
Database: PDB / ID: 4ili
TitleCrystal structure of an Aar2p S253E phosphomimetic mutant protein
ComponentsA1 cistron-splicing factor AAR2
KeywordsSPLICING / U5 snRNP assembly / Aar2 / Prp8
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: 3.2046 Å
AuthorsWeber, G. / Heroven, 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 1.2Sep 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

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Assembly

Deposited unit
A: A1 cistron-splicing factor AAR2
B: A1 cistron-splicing factor AAR2


Theoretical massNumber of molelcules
Total (without water)74,0992
Polymers74,0992
Non-polymers00
Water0
1
A: A1 cistron-splicing factor AAR2


Theoretical massNumber of molelcules
Total (without water)37,0501
Polymers37,0501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: A1 cistron-splicing factor AAR2


Theoretical massNumber of molelcules
Total (without water)37,0501
Polymers37,0501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.820, 62.820, 326.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein A1 cistron-splicing factor AAR2


Mass: 37049.664 Da / Num. of mol.: 2 / Mutation: S253E
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

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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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 40 mM imidazole, pH 7.75, 0.95 M sodium potassium tartrate and 0.2 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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 13, 2012
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: 3.2→50 Å / Num. all: 13156 / Num. obs: 13092 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.113 / Rsym value: 0.099 / Net I/σ(I): 14
Reflection shellResolution: 3.2→3.29 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 2 / Rsym value: 0.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SBT

3sbt


Resolution: 3.2046→45.259 Å / SU ML: 0.44 / σ(F): 1.99 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3054 663 5.06 %
Rwork0.2604 --
obs0.2627 13090 99.61 %
all-13156 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2046→45.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4831 0 0 0 4831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024960
X-RAY DIFFRACTIONf_angle_d0.5846699
X-RAY DIFFRACTIONf_dihedral_angle_d11.7321826
X-RAY DIFFRACTIONf_chiral_restr0.044695
X-RAY DIFFRACTIONf_plane_restr0.002865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2046-3.4520.37121270.32722392X-RAY DIFFRACTION99
3.452-3.79920.3361370.29222424X-RAY DIFFRACTION100
3.7992-4.34860.29961280.24912466X-RAY DIFFRACTION100
4.3486-5.47720.2811330.24392495X-RAY DIFFRACTION100
5.4772-45.26330.29011380.24642650X-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)
13.7297-0.6684-2.50665.04232.03637.0976-0.4669-2.06340.19481.0064-0.24530.93180.4729-0.57780.62950.82530.13860.25881.7229-0.24141.0934-32.389118.546424.2596
22.64842.3966-3.02983.9616-2.01277.7350.21370.04110.4759-0.59390.07540.1742-0.7833-0.8145-0.32230.94260.4615-0.07580.9315-0.16861.1169-27.242327.64171.2404
37.60291.04520.10518.097-1.78734.8927-0.08460.13990.086-0.7504-0.1499-0.6505-0.3168-0.13370.21120.51030.22420.03020.4839-0.13150.569-13.443719.35223.9159
42.4087-3.5671.7438.5637-2.88065.42670.30931.1954-1.6814-0.4647-0.03290.12890.0979-0.4156-0.05270.64170.18690.14570.8121-0.14370.9631-11.58265.69760.6368
59.19981.3851-2.65893.5821-3.33493.5125-0.2822-0.34450.35660.2426-0.3207-1.5912-0.23841.18330.561.0634-0.039-0.00441.66820.00891.09223.583230.819229.3869
64.41362.6815-2.66337.9412-2.72822.93510.3427-0.0606-0.05580.2428-0.4036-0.0847-0.3171-0.04160.14121.0413-0.022-0.21.376-0.04670.8462-4.74530.074126.8335
73.04-1.3788-5.42150.49262.60489.33120.2609-0.9751-0.24550.4309-0.03680.1542-0.93730.7207-0.59081.19990.1445-0.02621.60450.01410.8959-13.718434.031952.7895
86.3018-0.2262-2.0555.787-2.20922.2484-0.8895-1.2395-0.97321.54670.72030.13820.47950.25490.35461.84480.51240.06871.81880.08480.8716-8.175119.972350.9351
97.67-1.0818-5.19292.8934-2.24656.65220.014-0.8908-1.99891.0517-1.9449-1.4812-0.7819-1.55472.0431.62010.17030.03162.87870.13041.7783-0.532915.042557.8055
105.79215.54265.46465.37825.22425.10121.3379-0.2479-2.2111-1.8535-2.4413-4.6735-0.3023-0.49341.4091.98830.2996-0.1942.3510.56532.31233.18479.107254.1233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:122)
2X-RAY DIFFRACTION2chain 'A' and (resseq 123:204)
3X-RAY DIFFRACTION3chain 'A' and (resseq 205:273)
4X-RAY DIFFRACTION4chain 'A' and (resseq 274:318)
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:55)
6X-RAY DIFFRACTION6chain 'B' and (resseq 56:122)
7X-RAY DIFFRACTION7chain 'B' and (resseq 123:217)
8X-RAY DIFFRACTION8chain 'B' and (resseq 218:273)
9X-RAY DIFFRACTION9chain 'B' and (resseq 274:302)
10X-RAY DIFFRACTION10chain 'B' and (resseq 303:316)

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