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- PDB-3vah: Structure of U2AF65 variant with BrU3C4 DNA -

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Basic information

Entry
Database: PDB / ID: 3vah
TitleStructure of U2AF65 variant with BrU3C4 DNA
Components
  • DNA 5'-D(P*UP*UP*(BRU)P*CP*UP*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 / FOURIER SYNTHESIS / Resolution: 2.5 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
E: DNA 5'-D(P*UP*UP*(BRU)P*CP*UP*UP*U)-3'
P: DNA 5'-D(P*UP*UP*(BRU)P*CP*UP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,06715
Polymers42,2804
Non-polymers1,78711
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.238, 37.304, 101.310
Angle α, β, γ (deg.)90.000, 125.610, 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 ABEP

#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(P*UP*UP*(BRU)P*CP*UP*UP*U)-3'


Mass: 2064.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA

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Non-polymers , 5 types, 106 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.: 5 / Source method: obtained synthetically / Formula: SO4
#5: 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
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.02 Å3/Da / Density % sol: 59.27 %
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: CHESS / Beamline: A1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 25, 2007 / Details: Rh coated Si vertical focus mirror
RadiationMonochromator: Horizontal focusing 5.05? asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 17610 / % possible obs: 99.3 % / Observed criterion σ(I): -1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.114 / Χ2: 1.895 / Net I/σ(I): 19.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.594.40.43517141.349199.7
2.59-2.694.50.35417391.557199.7
2.69-2.824.50.317651.629199.7
2.82-2.964.70.23217271.771199.9
2.96-3.154.80.18717781.992199.6
3.15-3.394.80.13617642.005199.6
3.39-3.734.60.11317552.54199.3
3.73-4.274.50.0917582.285198.8
4.27-5.384.40.07517801.983198.9
5.38-504.30.06818301.785197.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→41.17 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 18.082 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.576 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 1693 10 %RANDOM
Rwork0.1976 ---
obs0.2035 16939 94.42 %-
all-18632 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.5 Å2 / Biso mean: 34.1778 Å2 / Biso min: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å21.07 Å2
2---1.89 Å20 Å2
3---3.61 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 208 82 95 3071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223147
X-RAY DIFFRACTIONr_bond_other_d0.0130.022083
X-RAY DIFFRACTIONr_angle_refined_deg1.3612.1174300
X-RAY DIFFRACTIONr_angle_other_deg0.94435090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90124.923130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76515460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2671514
X-RAY DIFFRACTIONr_chiral_restr0.0690.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02557
X-RAY DIFFRACTIONr_nbd_refined0.2290.2488
X-RAY DIFFRACTIONr_nbd_other0.1930.21944
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21425
X-RAY DIFFRACTIONr_nbtor_other0.0830.21541
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.4030.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2650.25
X-RAY DIFFRACTIONr_mcbond_it0.5591.52207
X-RAY DIFFRACTIONr_mcbond_other0.0851.5712
X-RAY DIFFRACTIONr_mcangle_it0.65622742
X-RAY DIFFRACTIONr_scbond_it1.23231684
X-RAY DIFFRACTIONr_scangle_it1.9364.51558
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 102 -
Rwork0.274 840 -
all-942 -
obs--74.53 %
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)
12.81311.76760.18082.4576-0.75134.2445-0.10890.1504-0.2686-0.0836-0.0552-0.08780.10610.0820.1641-0.1703-0.03230.0181-0.1917-0.057-0.122-11.3371-20.045231.1604
29.74771.83820.22133.83630.45644.464-0.0010.1771-0.0213-0.28860.11020.1411-0.13760.1124-0.1092-0.1692-0.08010.0376-0.2193-0.0405-0.1413-33.0885.66927.0658
36.16311.88860.43034.4105-0.41113.9011-0.25280.13850.0365-0.24310.19630.16070.1542-0.23130.0565-0.1984-0.015-0.0415-0.21170.0002-0.160725.4787-27.780829.1
46.80240.83562.13834.5330.41947.0756-0.10780.49790.1232-0.24030.0726-0.3151-0.354-0.0120.0352-0.1001-0.09660.0309-0.08120.0033-0.24154.6689-4.073913.91
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A143 - 237
2X-RAY DIFFRACTION2A258 - 336
3X-RAY DIFFRACTION3B143 - 237
4X-RAY DIFFRACTION4B258 - 336

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