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- PDB-5ev2: Structure II of Intact U2AF65 Recognizing the 3' Splice Site Signal -

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Basic information

Entry
Database: PDB / ID: 5ev2
TitleStructure II of Intact U2AF65 Recognizing the 3' Splice Site Signal
Components
  • DNA (5'-R(P*UP*U)-D(P*UP*U)-R(P*U)-D(P*UP*(BRU)P*U)-3')
  • Splicing factor U2AF 65 kDa subunit
KeywordsRNA BINDING PROTEIN/RNA / PROTEIN-RNA COMPLEX / RNA SPLICING FACTOR / RNA RECOGNITION MOTIF / POLYPYRIMIDINE TRACT / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA 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 / 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
1,4-DIETHYLENE DIOXIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / DNA/RNA hybrid / Splicing factor U2AF 65 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic Construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.86 Å
AuthorsAgrawal, A.A. / Jenkins, J.L. / Kielkopf, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM070503 United States
CitationJournal: Nat Commun / Year: 2016
Title: An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal.
Authors: Agrawal, A.A. / Salsi, E. / Chatrikhi, R. / Henderson, S. / Jenkins, J.L. / Green, M.R. / Ermolenko, D.N. / Kielkopf, C.L.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,7185
Polymers24,3732
Non-polymers3443
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-16 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.469, 115.220, 59.544
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-635-

HOH

21A-652-

HOH

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Components

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Protein / DNA/RNA hybrid , 2 types, 2 molecules AB

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


Mass: 21970.004 Da / Num. of mol.: 1 / Fragment: UNP residues 141-341
Source method: isolated from a genetically manipulated source
Details: 5' PHOSPHORYLATION / Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Plasmid: PGEX-6P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P26368
#2: DNA/RNA hybrid DNA (5'-R(P*UP*U)-D(P*UP*U)-R(P*U)-D(P*UP*(BRU)P*U)-3')


Mass: 2403.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic Construct (others)

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Non-polymers , 4 types, 206 molecules

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


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200 mM LiCl, 100 mM sodium citrate, 8% PEG 6000, 10% PEG 300, 10% Dioxane, Deoxy-BigCHAP
PH range: 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.1042 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1042 Å / Relative weight: 1
ReflectionResolution: 1.86→32.57 Å / Num. obs: 17870 / % possible obs: 98.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 22.27 Å2 / Rsym value: 0.039 / Net I/σ(I): 24.6
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 4.6 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.1.26data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
Blu-Icedata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.86→32.57 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 18.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 1456 8 %
Rwork0.151 --
obs0.154 17870 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.48 Å2
Refinement stepCycle: LAST / Resolution: 1.86→32.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 156 23 203 1903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011756
X-RAY DIFFRACTIONf_angle_d1.1162399
X-RAY DIFFRACTIONf_dihedral_angle_d14.561060
X-RAY DIFFRACTIONf_chiral_restr0.06270
X-RAY DIFFRACTIONf_plane_restr0.008291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8594-1.89320.27181480.22191506X-RAY DIFFRACTION94
1.8932-1.92960.26711460.20851624X-RAY DIFFRACTION97
1.9296-1.9690.26761260.20721663X-RAY DIFFRACTION98
1.969-2.01180.21371510.18261572X-RAY DIFFRACTION98
2.0118-2.05860.22161450.17341650X-RAY DIFFRACTION97
2.0586-2.110.18531460.15961631X-RAY DIFFRACTION98
2.11-2.16710.23721240.15661611X-RAY DIFFRACTION98
2.1671-2.23080.20261480.14881634X-RAY DIFFRACTION98
2.2308-2.30280.17851360.14781644X-RAY DIFFRACTION98
2.3028-2.38510.16271640.14021640X-RAY DIFFRACTION98
2.3851-2.48060.19351320.14161623X-RAY DIFFRACTION98
2.4806-2.59340.18741380.14761663X-RAY DIFFRACTION99
2.5934-2.73010.21781480.14331626X-RAY DIFFRACTION99
2.7301-2.9010.17951390.14991639X-RAY DIFFRACTION99
2.901-3.12490.21641380.14131652X-RAY DIFFRACTION98
3.1249-3.4390.18521530.13961650X-RAY DIFFRACTION99
3.439-3.93590.15311320.13311634X-RAY DIFFRACTION99
3.9359-4.9560.14141350.12491677X-RAY DIFFRACTION99
4.956-32.57650.1841450.17861645X-RAY DIFFRACTION99

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