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- PDB-4tu9: STRUCTURE OF U2AF65 VARIANT WITH BRU5G6 DNA -

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Basic information

Entry
Database: PDB / ID: 4tu9
TitleSTRUCTURE OF U2AF65 VARIANT WITH BRU5G6 DNA
Components
  • DNA (5'-D(*UP*UP*UP*UP*(BRU)P*DG*U)-3')
  • Splicing factor U2AF 65 kDa subunit
KeywordsRNA BINDING PROTEIN/DNA / RNA SPLICING FACTOR / RNA RECOGNITION MOTIF / RNA BINDING PROTEIN / RNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / C2H2 zinc finger domain binding / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity ...U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / C2H2 zinc finger domain binding / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity / Protein hydroxylation / negative regulation of mRNA splicing, via spliceosome / negative regulation of protein ubiquitination / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / nuclear speck / enzyme binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
U2 snRNP auxilliary factor, large subunit, splicing factor / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / DNA / Splicing factor U2AF 65 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.992 Å
AuthorsJenkins, J.L. / McLaughlin, K.J. / Agrawal, A.A. / Kielkopf, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure-guided U2AF65 variant improves recognition and splicing of a defective pre-mRNA.
Authors: Agrawal, A.A. / McLaughlin, K.J. / Jenkins, J.L. / Kielkopf, C.L.
History
DepositionJun 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Dec 2, 2015Group: Structure summary
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Splicing factor U2AF 65 kDa subunit
B: Splicing factor U2AF 65 kDa subunit
P: DNA (5'-D(*UP*UP*UP*UP*(BRU)P*DG*U)-3')
E: DNA (5'-D(*UP*UP*UP*UP*(BRU)P*DG*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,42318
Polymers42,3604
Non-polymers2,06314
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.488, 37.183, 101.047
Angle α, β, γ (deg.)90.000, 125.570, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

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Components

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Protein / DNA chain , 2 types, 4 molecules ABPE

#1: Protein Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / hU2AF65 / U2 snRNP auxiliary factor large subunit


Mass: 19075.754 Da / Num. of mol.: 2 / Fragment: UNP residues 148-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Plasmid: PGEX-6P / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P26368
#2: DNA chain DNA (5'-D(*UP*UP*UP*UP*(BRU)P*DG*U)-3')


Mass: 2104.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 279 molecules

#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CPQ / N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE / DEOXY-BIGCHAP


Mass: 862.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H75N3O15 / Comment: detergent*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M AMMONIUM SULFATE, 10% DIOXANE, 0.1M MES PH 6.5, DEOXY-BIG CHAP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.992→30 Å / Num. obs: 33992 / % possible obs: 99.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 28.98 Å2 / Net I/σ(I): 18.421
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.992-2.032.60.44516711.34398.7
2.03-2.072.50.56616793.33998.2
2.07-2.112.60.43916672.1298.8
2.11-2.152.60.30416591.57999.2
2.15-2.22.60.26217201.36599.5
2.2-2.252.50.3516543.78297.9
2.25-2.312.60.28216852.21398.7
2.31-2.372.60.18816701.59399.3
2.37-2.442.60.15717101.50499.9
2.44-2.522.60.14116871.5499.7
2.52-2.612.60.12517151.53899.5
2.61-2.712.60.12916682.18998.9
2.71-2.842.60.0917471.47699.5
2.84-2.992.60.0716731.24399.5
2.99-3.172.60.06217241.39399.6
3.17-3.422.60.04917091.46499.5
3.42-3.762.60.04317231.55999.3
3.76-4.312.60.03317041.16999.1
4.31-5.422.60.02617600.93199.4
5.42-302.50.02617670.9196.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.992→29.069 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 3362 9.91 %
Rwork0.1875 30559 -
obs0.1922 33921 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.83 Å2 / Biso mean: 34.5306 Å2 / Biso min: 12.32 Å2
Refinement stepCycle: final / Resolution: 1.992→29.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 234 103 265 3288
Biso mean--52.44 39.97 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073180
X-RAY DIFFRACTIONf_angle_d1.2054355
X-RAY DIFFRACTIONf_chiral_restr0.045473
X-RAY DIFFRACTIONf_plane_restr0.004516
X-RAY DIFFRACTIONf_dihedral_angle_d20.071296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.992-2.02080.32431160.2567987110378
2.0208-2.05090.30061470.25721278142599
2.0509-2.0830.40431190.31541246136595
2.083-2.11710.28791360.2351272140899
2.1171-2.15360.28471330.22491274140799
2.1536-2.19280.27471360.22071309144599
2.1928-2.23490.26621410.23051227136899
2.2349-2.28050.4051430.2961246138995
2.2805-2.33010.27391450.2031265141099
2.3301-2.38430.29371270.197412891416100
2.3843-2.44390.25191480.197712791427100
2.4439-2.50990.25211300.186813001430100
2.5099-2.58370.23351670.20312441411100
2.5837-2.66710.27231340.2021312144699
2.6671-2.76230.27341350.20591284141999
2.7623-2.87280.25731490.20891280142999
2.8728-3.00340.2711460.184113071453100
3.0034-3.16160.22991510.18712761427100
3.1616-3.35940.23641590.18212941453100
3.3594-3.61840.19941430.16511288143199
3.6184-3.98170.19121450.14931292143799
3.9817-4.55590.15921370.139513221459100
4.5559-5.73280.19871380.16091331146999
5.7328-29.07250.20251370.19681357149496

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