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- PDB-4yh8: Structure of yeast U2AF complex -

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Basic information

Entry
Database: PDB / ID: 4yh8
TitleStructure of yeast U2AF complex
Components
  • Splicing factor U2AF 23 kDa subunit
  • Splicing factor U2AF 59 kDa subunit
KeywordsSPLICING / RRM / Zn-finger / 3' splice site
Function / homology
Function and homology information


mRNA branch site recognition / U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / spliceosomal complex ...mRNA branch site recognition / U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / spliceosomal complex / mRNA splicing, via spliceosome / nuclear speck / mRNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
U2 auxiliary factor small subunit / U2 snRNP auxilliary factor, large subunit, splicing factor / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / RNA recognition motif domain, eukaryote / RNA recognition motif / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / RNA recognition motif / RNA recognition motif ...U2 auxiliary factor small subunit / U2 snRNP auxilliary factor, large subunit, splicing factor / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / RNA recognition motif domain, eukaryote / RNA recognition motif / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Splicing factor U2AF 59 kDa subunit / Splicing factor U2AF 23 kDa subunit
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYoshida, H. / Park, S.Y. / Urano, T. / Obayashi, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology20112006 Japan
CitationJournal: Genes Dev. / Year: 2015
Title: A novel 3' splice site recognition by the two zinc fingers in the U2AF small subunit.
Authors: Yoshida, H. / Park, S.Y. / Oda, T. / Akiyoshi, T. / Sato, M. / Shirouzu, M. / Tsuda, K. / Kuwasako, K. / Unzai, S. / Muto, Y. / Urano, T. / Obayashi, E.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor U2AF 23 kDa subunit
B: Splicing factor U2AF 59 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1404
Polymers33,0092
Non-polymers1312
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-26 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.616, 112.704, 57.198
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-445-

HOH

21B-218-

HOH

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Components

#1: Protein Splicing factor U2AF 23 kDa subunit / U2 auxiliary factor 23 kDa subunit / U2AF23 / U2 snRNP auxiliary factor small subunit


Mass: 25066.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: SPAP8A3.06 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09176
#2: Protein Splicing factor U2AF 59 kDa subunit / U2 auxiliary factor 59 kDa subunit / U2AF59 / U2 snRNP auxiliary factor large subunit


Mass: 7942.985 Da / Num. of mol.: 1 / Fragment: UNP residues 93-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: prp2, mis11, SPBC146.07 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: P36629
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG 1000, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 32806 / % possible obs: 99.1 % / Redundancy: 8.4 % / Net I/σ(I): 33.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.5 / % possible all: 90.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1692)phasing
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→35.545 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 1583 4.83 %
Rwork0.1912 --
obs0.1924 32782 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→35.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 2 208 2136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081971
X-RAY DIFFRACTIONf_angle_d1.0532658
X-RAY DIFFRACTIONf_dihedral_angle_d15.837757
X-RAY DIFFRACTIONf_chiral_restr0.041272
X-RAY DIFFRACTIONf_plane_restr0.005353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.697-1.75180.29671330.25582511X-RAY DIFFRACTION89
1.7518-1.81440.2791620.24012790X-RAY DIFFRACTION99
1.8144-1.88710.25991420.22632830X-RAY DIFFRACTION100
1.8871-1.97290.2541270.21422865X-RAY DIFFRACTION100
1.9729-2.0770.26151460.20322818X-RAY DIFFRACTION100
2.077-2.20710.21571500.20272859X-RAY DIFFRACTION100
2.2071-2.37740.20661430.19912848X-RAY DIFFRACTION100
2.3774-2.61660.23991410.20212864X-RAY DIFFRACTION100
2.6166-2.99510.22861540.20212871X-RAY DIFFRACTION100
2.9951-3.77280.2131230.1842923X-RAY DIFFRACTION100
3.7728-35.55320.18411620.16673020X-RAY DIFFRACTION100

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