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- PDB-3vam: Structure of U2AF65 variant with BrU5C2 DNA -

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Basic information

Entry
Database: PDB / ID: 3vam
TitleStructure of U2AF65 variant with BrU5C2 DNA
Components
  • DNA (5'-D(*UP*CP*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 / FOURIER SYNTHESIS / Resolution: 2.4 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
P: DNA (5'-D(*UP*CP*UP*UP*(BRU)P*UP*U)-3')
E: DNA (5'-D(*UP*CP*UP*UP*(BRU)P*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,24717
Polymers42,2804
Non-polymers1,96713
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.108, 37.973, 101.974
Angle α, β, γ (deg.)90.000, 125.490, 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*CP*UP*UP*(BRU)P*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, 140 molecules

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


Mass: 88.105 Da / Num. of mol.: 5 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / 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.: 127 / 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: 3.1 Å3/Da / Density % sol: 60.28 %
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: Jan 1, 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: 2.4→50 Å / Num. obs: 20311 / % possible obs: 99.5 % / Observed criterion σ(I): -1 / Redundancy: 5.1 % / Rmerge(I) obs: 0.086 / Χ2: 1.619 / Net I/σ(I): 22
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.494.80.40119881.156199.8
2.49-2.595.20.36220201.2271100
2.59-2.75.30.24920331.358199.9
2.7-2.855.30.19819991.504199.8
2.85-3.025.30.15120261.717199.8
3.02-3.265.30.11420231.99199.6
3.26-3.585.20.08720152.054199.3
3.58-4.150.07120352.131198.9
4.1-5.174.90.06120471.617198.7
5.17-504.80.05621251.392198.9

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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: 2.4→41.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 13.171 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.4 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1911 9.9 %RANDOM
Rwork0.1938 ---
obs0.198 19317 93.02 %-
all-21228 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.97 Å2 / Biso mean: 41.9785 Å2 / Biso min: 20.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å21.06 Å2
2--0.97 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 230 94 127 3126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223100
X-RAY DIFFRACTIONr_bond_other_d0.0040.022063
X-RAY DIFFRACTIONr_angle_refined_deg1.3042.1024232
X-RAY DIFFRACTIONr_angle_other_deg0.90935046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32224.923130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48615463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9831514
X-RAY DIFFRACTIONr_chiral_restr0.0710.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02557
X-RAY DIFFRACTIONr_nbd_refined0.1760.2439
X-RAY DIFFRACTIONr_nbd_other0.1850.21905
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21378
X-RAY DIFFRACTIONr_nbtor_other0.0820.21544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0880.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.26
X-RAY DIFFRACTIONr_mcbond_it0.5321.52208
X-RAY DIFFRACTIONr_mcbond_other0.0751.5709
X-RAY DIFFRACTIONr_mcangle_it0.63222738
X-RAY DIFFRACTIONr_scbond_it1.21231629
X-RAY DIFFRACTIONr_scangle_it1.9794.51493
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 104 -
Rwork0.259 893 -
all-997 -
obs--66.16 %
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)
12.46231.6125-0.97983.6605-0.93494.66140.00610.0348-0.2328-0.0808-0.1196-0.05120.0952-0.16720.1134-0.2182-0.0203-0.0127-0.1321-0.0252-0.1509-11.4618-19.790131.3444
28.49761.14981.15491.88020.05812.95280.01740.0277-0.024-0.11880.0986-0.3139-0.25490.2423-0.1159-0.1052-0.08520.0629-0.1358-0.0605-0.1125-33.02336.069826.9849
34.01832.0237-0.2515.7894-0.69472.7276-0.1523-0.0527-0.04-0.33590.23240.21230.1444-0.1485-0.0801-0.1913-0.0408-0.0348-0.14960.0039-0.193625.9442-28.468329.1097
46.80711.81942.55293.27650.54558.178-0.2120.30540.2262-0.36710.192-0.144-0.67030.10760.02-0.0878-0.06470.0161-0.14090.0122-0.23214.7049-3.958313.9343
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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