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- PDB-3val: Structure of U2AF65 variant with BrU5C1 DNA -

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Basic information

Entry
Database: PDB / ID: 3val
TitleStructure of U2AF65 variant with BrU5C1 DNA
Components
  • DNA (5'-D(*C*UP*UP*UP*(BRU)P*UP*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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJenkins, J.L. / Frato, K.H. / Kielkopf, C.L.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs.
Authors: Jenkins, J.L. / Agrawal, A.A. / Gupta, A. / Green, M.R. / Kielkopf, C.L.
History
DepositionDec 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
D: Splicing factor U2AF 65 kDa subunit
I: Splicing factor U2AF 65 kDa subunit
E: DNA (5'-D(*C*UP*UP*UP*(BRU)P*UP*U)-3')
H: DNA (5'-D(*C*UP*UP*UP*(BRU)P*UP*U)-3')
K: DNA (5'-D(*C*UP*UP*UP*(BRU)P*UP*U)-3')
P: DNA (5'-D(*C*UP*UP*UP*(BRU)P*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,96923
Polymers84,5608
Non-polymers1,40915
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.583, 137.081, 83.962
Angle α, β, γ (deg.)90.00, 102.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / hU2AF(65) / hU2AF65 / U2 snRNP auxiliary factor large subunit


Mass: 19075.754 Da / Num. of mol.: 4 / Fragment: RNA Binding Domains 1 and 2
Source method: isolated from a genetically manipulated source
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 chain
DNA (5'-D(*C*UP*UP*UP*(BRU)P*UP*U)-3')


Mass: 2064.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA
#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


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


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
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, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.912 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / % possible obs: 95.1 % / Observed criterion σ(I): -1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.147 / Χ2: 1.635 / Net I/σ(I): 17.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.593.90.32419280.448169.1
2.59-2.694.70.30125000.52185.7
2.69-2.825.80.27527100.598196.1
2.82-2.966.90.2428230.72199.5
2.96-3.157.50.19828720.939199.8
3.15-3.397.60.16428611.4991100
3.39-3.737.50.14828422.2971100
3.73-4.277.40.1428622.571100
4.27-5.387.10.13428872.611100
5.38-307.50.11529042.4091100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G4B

2g4b


Resolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2706 4926 8.7 %RANDOM
Rwork0.2079 ---
all-55742 --
obs-50816 90.1 %-
Solvent computationBsol: 38.3339 Å2
Displacement parametersBiso max: 123.62 Å2 / Biso mean: 39.7133 Å2 / Biso min: 10.82 Å2
Baniso -1Baniso -2Baniso -3
1-3.968 Å20 Å20.446 Å2
2---16.729 Å20 Å2
3---12.761 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5357 441 79 225 6102
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0072
X-RAY DIFFRACTIONc_angle_deg1.232.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.52.5
X-RAY DIFFRACTIONc_improper_angle_d0.963
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep_brpatch.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION5dioxane.param

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