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- PDB-3vaf: Structure of U2AF65 variant with BrU3 DNA -

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Basic information

Entry
Database: PDB / ID: 3vaf
TitleStructure of U2AF65 variant with BrU3 DNA
Components
  • DNA 5'-D(*UP*UP*(BRU)P*(BRU)P*UP*UP*U)-3'
  • Splicing factor U2AF 65 kDa subunit
KeywordsRNA BINDING PROTEIN/DNA / RNA SPLICING FACTOR / RNA RECOGNITION MOTIF / 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: 2.49 Å
AuthorsJenkins, J.L. / 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
P: DNA 5'-D(*UP*UP*(BRU)P*(BRU)P*UP*UP*U)-3'
E: DNA 5'-D(*UP*UP*(BRU)P*(BRU)P*UP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,32216
Polymers42,4404
Non-polymers1,88312
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.296, 36.981, 99.431
Angle α, β, γ (deg.)90.000, 125.670, 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 / hU2AF(65) / hU2AF65 / U2 snRNP auxiliary factor large subunit


Mass: 19075.754 Da / Num. of mol.: 2 / 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(*UP*UP*(BRU)P*(BRU)P*UP*UP*U)-3'


Mass: 2144.002 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA

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Non-polymers , 5 types, 131 molecules

#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.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / 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


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPROTEIN WAS COCRYSTALIZED WITH A DNA 7MER (5'-D(*UP*UP*(BRU)P*UP*UP*UP*U)-3') BUT THE PROTEIN BOUND ...PROTEIN WAS COCRYSTALIZED WITH A DNA 7MER (5'-D(*UP*UP*(BRU)P*UP*UP*UP*U)-3') BUT THE PROTEIN BOUND THE DNA IN DIFFERENT REGISTERS RESULTING IN THE BRU APPEARING IN MORE THAN ONE POSITION IN THE STRUCTURE

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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: 2.89 Å3/Da / Density % sol: 57.46 %
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, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 17441 / % possible obs: 99.3 % / Observed criterion σ(I): -1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 18.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
2.49-2.584.70.4551612199.3
2.58-2.686.30.4741762195.2
2.68-2.86.60.39717291100
2.8-2.956.90.24517401100
2.95-3.1470.18917431100
3.14-3.387.10.15517541100
3.38-3.7270.15317521100
3.72-4.266.90.12417481100
4.26-5.366.90.08517851100
5.36-506.40.0761816198.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G4B

2g4b


Resolution: 2.49→20.51 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.869 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 17.959 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.705 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2886 1617 9.9 %RANDOM
Rwork0.2305 ---
obs0.2361 16380 93.5 %-
all-17997 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.44 Å2 / Biso mean: 35.2124 Å2 / Biso min: 15.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20.5 Å2
2--0.23 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 2.49→20.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 226 87 119 3107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223068
X-RAY DIFFRACTIONr_bond_other_d0.0050.022044
X-RAY DIFFRACTIONr_angle_refined_deg1.4012.0894187
X-RAY DIFFRACTIONr_angle_other_deg1.09334992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57924.885131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17915461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2321514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02563
X-RAY DIFFRACTIONr_nbd_refined0.2160.2582
X-RAY DIFFRACTIONr_nbd_other0.1960.22091
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21463
X-RAY DIFFRACTIONr_nbtor_other0.0860.21588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0410.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.24
X-RAY DIFFRACTIONr_mcbond_it0.5091.52194
X-RAY DIFFRACTIONr_mcbond_other0.0821.5709
X-RAY DIFFRACTIONr_mcangle_it0.63322738
X-RAY DIFFRACTIONr_scbond_it1.14931589
X-RAY DIFFRACTIONr_scangle_it1.7934.51448
LS refinement shellResolution: 2.486→2.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 96 -
Rwork0.371 963 -
all-1059 -
obs--84.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.56721.25670.86472.0747-0.00475.0989-0.16870.0848-0.2822-0.0414-0.06780.04070.17590.00480.2365-0.176-0.04970.0296-0.1834-0.0855-0.117913.112790.3588111.3416
27.83131.87961.71682.457-0.18694.6975-0.02760.06890.0398-0.21960.2429-0.0119-0.33480.1414-0.2154-0.0964-0.14240.1095-0.1393-0.11660.0194-8.1753115.5543107.0935
35.44160.43450.47355.9848-0.87363.7806-0.25280.01350.0561-0.43380.29850.23820.233-0.2285-0.0457-0.1823-0.058-0.0156-0.15380.0051-0.190850.06882.1884109.2609
46.34991.93532.03144.5845-0.44056.0914-0.28770.51560.0466-0.31860.1226-0.0789-0.41360.010.1652-0.1099-0.0509-0.0179-0.06430.0105-0.247629.0005106.198494.3352
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A143 - 237
2X-RAY DIFFRACTION2A258 - 336
3X-RAY DIFFRACTION3B145 - 237
4X-RAY DIFFRACTION4B258 - 336

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