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- PDB-5ev1: Structure I of Intact U2AF65 Recognizing a 3' Splice Site Signal -

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Basic information

Entry
Database: PDB / ID: 5ev1
TitleStructure I of Intact U2AF65 Recognizing a 3' Splice Site Signal
Components
  • DNA/RNA (5'-R(*UP*UP*U)-D(P*UP*UP*(BRU)P*U)-R(P*UP*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 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.037 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 1.4Sep 27, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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: DNA/RNA (5'-R(*UP*UP*U)-D(P*UP*UP*(BRU)P*U)-R(P*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9986
Polymers24,6952
Non-polymers3024
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-13 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.052, 114.241, 59.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-401-

NA

21B-101-

NA

31A-572-

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
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/RNA (5'-R(*UP*UP*U)-D(P*UP*UP*(BRU)P*U)-R(P*UP*U)-3')


Mass: 2725.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The 3' U is disordered in this 9mer / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 122 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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.: 118 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM phosphate-citrate buffer, 40% Peg400, 10% dioxane
PH range: 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.037→32.456 Å / Num. obs: 13202 / % possible obs: 95.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 35.26 Å2 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.019 / Rrim(I) all: 0.044 / Net I/av σ(I): 13.688 / Net I/σ(I): 21.2 / Num. measured all: 61150
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.037-2.154.10.3212.3626915440.1710.3214.278.3
2.15-2.284.80.223.4891818500.1080.226.599.1
2.28-2.444.70.1584.7836717680.0770.1588.999.3
2.44-2.634.90.1086.7780916100.0520.10812.298.2
2.63-2.884.80.07110.4723415180.0350.07117.898.8
2.88-3.224.60.04515.6633013630.0220.04526.998
3.22-3.724.70.03120.5577812320.0150.03138.999.2
3.72-4.564.60.02325.9469810260.0120.02348.797.4
4.56-6.444.50.02324.836548160.0120.02348.897.5
6.44-32.4564.40.0222520934750.0110.02250.995.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.15data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G4B

2g4b


Resolution: 2.037→32.456 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.89 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 1055 7.96 %
Rwork0.1734 22478 -
obs0.1778 12124 93.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.23 Å2 / Biso mean: 47.2807 Å2 / Biso min: 20.11 Å2
Refinement stepCycle: final / Resolution: 2.037→32.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 154 19 118 1796
Biso mean--54.52 45.24 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131719
X-RAY DIFFRACTIONf_angle_d1.322353
X-RAY DIFFRACTIONf_chiral_restr0.069268
X-RAY DIFFRACTIONf_plane_restr0.009286
X-RAY DIFFRACTIONf_dihedral_angle_d14.6771027
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0373-2.08830.3534940.2715973106758
2.0883-2.14470.31371320.24291558169090
2.1447-2.20780.34161380.23321671180998
2.2078-2.27910.25911590.21941640179997
2.2791-2.36050.32231380.20891664180298
2.3605-2.4550.29281440.20591682182696
2.455-2.56670.22871420.20641633177596
2.5667-2.70190.24331560.18211699185598
2.7019-2.87110.23391290.19941656178597
2.8711-3.09270.25391410.19251642178396
3.0927-3.40360.24241470.17471686183398
3.4036-3.89540.20171450.14871661180697
3.8954-4.90510.1561360.13241659179597
4.9051-32.46010.22181430.15941654179796

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