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- PDB-4tu8: STRUCTURE OF U2AF65 VARIANT WITH BRU5A6 DNA -

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Basic information

Entry
Database: PDB / ID: 4tu8
TitleSTRUCTURE OF U2AF65 VARIANT WITH BRU5A6 DNA
Components
  • DNA (5'-D(*UP*UP*UP*UP*(BRU)P*DA*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 / spliceosomal complex assembly / 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 / FOURIER SYNTHESIS / Resolution: 1.918 Å
AuthorsMCLAUGHLIN, K.J. / JENKINS, J.L. / Agrawal, A.A. / KIELKOPF, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM070503 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)RR026501 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 3, 2014Group: Derived calculations
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Dec 24, 2014Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.6Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.7Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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*DA*U)-3')
E: DNA (5'-D(*UP*UP*UP*UP*(BRU)P*DA*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,74525
Polymers42,3284
Non-polymers2,41821
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint4 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.040, 37.178, 100.710
Angle α, β, γ (deg.)90.000, 125.660, 90.000
Int Tables number5
Space group name H-MC121

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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*DA*U)-3')


Mass: 2088.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 316 molecules

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


Mass: 88.105 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.98 Å3/Da / Density % sol: 58.72 %
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, ETHYLENE GLYCOL, 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: May 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.918→31.07 Å / Num. obs: 70516 / % possible obs: 94.3 % / Redundancy: 2.8 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.086 / Net I/av σ(I): 11.8 / Net I/σ(I): 11 / Num. measured all: 107030
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.918-1.952.50.42823861.02964.3
1.95-1.991.40.42236101.13195.9
1.99-2.031.50.36235761.09895.9
2.03-2.071.50.32936291.1496.4
2.07-2.111.50.28635581.15995.6
2.11-2.161.50.2336341.12896.6
2.16-2.221.50.19336271.11696.6
2.22-2.281.50.18735151.15195.6
2.28-2.341.50.1736761.06996.7
2.34-2.421.50.14135591.07196.2
2.42-2.511.50.1236481.06896.7
2.51-2.611.50.10735561.06796.6
2.61-2.721.50.09436351.09296.3
2.72-2.871.50.08236151.02396.2
2.87-3.051.50.06835841.06896.6
3.05-3.281.50.05735951.11795.8
3.28-3.611.50.0535621.01995.2
3.61-4.141.50.04535361.07494.4
4.14-5.211.50.0435331.08594.5
5.21-501.60.03934821.01993

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.918→31.068 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 23.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 3775 9.92 %
Rwork0.1778 63501 -
obs0.1818 70496 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.97 Å2 / Biso mean: 39.7201 Å2 / Biso min: 21.52 Å2
Refinement stepCycle: final / Resolution: 1.918→31.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 247 145 295 3371
Biso mean--58.62 46.3 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073173
X-RAY DIFFRACTIONf_angle_d1.2234316
X-RAY DIFFRACTIONf_chiral_restr0.046470
X-RAY DIFFRACTIONf_plane_restr0.004515
X-RAY DIFFRACTIONf_dihedral_angle_d19.9231287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.918-1.93930.33371670.30021672183974
1.9393-1.96220.32092460.26642125237196
1.9622-1.98610.32492430.24952105234896
1.9861-2.01120.2572040.25692115231996
2.0112-2.03770.3092500.23562181243196
2.0377-2.06560.26592550.23062183243896
2.0656-2.09510.25782150.23832109232495
2.0951-2.12640.25182590.21342105236497
2.1264-2.15960.22892020.21372205240797
2.1596-2.1950.27092380.21032151238996
2.195-2.23280.27672450.20722088233396
2.2328-2.27340.24022290.21122161239095
2.2734-2.31710.2532580.19842129238797
2.3171-2.36440.28392040.20512147235196
2.3644-2.41580.24692370.20772137237497
2.4158-2.4720.24162610.19852212247397
2.472-2.53370.2732330.20462078231197
2.5337-2.60220.27732530.19552127238097
2.6022-2.67870.26782170.20392213243097
2.6787-2.76520.23152160.19452090230696
2.7652-2.86390.23182610.19672153241496
2.8639-2.97850.24352370.18832143238097
2.9785-3.11390.24592840.18552139242396
3.1139-3.27790.212350.17362065230096
3.2779-3.48310.2032420.16162150239295
3.4831-3.75160.16072230.14622115233894
3.7516-4.12830.17312530.13462071232495
4.1283-4.72390.15482010.12692129233094
4.7239-5.94480.18752260.1592123234995
5.9448-31.07190.21152010.18542080228192

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