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- PDB-7s3a: Crystal structure of intact U2AF65 RRM-region bound to AdML-C5 ol... -

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Basic information

Entry
Database: PDB / ID: 7s3a
TitleCrystal structure of intact U2AF65 RRM-region bound to AdML-C5 oligonucleotide
Components
  • DNA/RNA (5'-R(P*UP*UP*(UD)P*CP*U)-D(P*(BRU))-R(P*CP*C)-3')
  • Splicing factor U2AF 65 kDa subunit
KeywordsRNA BINDING PROTEIN/RNA/DNA / PROTEIN-RNA COMPLEX / RNA SPLICING FACTOR / RNA RECOGNITION MOTIF / POLYPYRIMIDINE TRACT / RNA BINDING PROTEIN-RNA-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
DNA/RNA hybrid / Splicing factor U2AF 65 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.48 Å
AuthorsJenkins, J.L. / Henderson, S. / Kielkopf, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM070503-15 United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal.
Authors: Glasser, E. / Maji, D. / Biancon, G. / Puthenpeedikakkal, A.M.K. / Cavender, C.E. / Tebaldi, T. / Jenkins, J.L. / Mathews, D.H. / Halene, S. / Kielkopf, C.L.
History
DepositionSep 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jun 29, 2022Group: Atomic model / Data collection / Polymer sequence / Category: atom_site / entity_poly / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_poly.type / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor U2AF 65 kDa subunit
B: DNA/RNA (5'-R(P*UP*UP*(UD)P*CP*U)-D(P*(BRU))-R(P*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7555
Polymers24,6862
Non-polymers693
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-50 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.245, 63.022, 77.491
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22237.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Details (production host): PGEX-6P / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P26368
#2: DNA/RNA hybrid DNA/RNA (5'-R(P*UP*UP*(UD)P*CP*U)-D(P*(BRU))-R(P*CP*C)-3')


Mass: 2448.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.60 M succinic acid, 0.10 M Hepes pH 7.0, 2% Peg MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2015
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.48→38.75 Å / Num. obs: 35972 / % possible obs: 98.7 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.026 / Rrim(I) all: 0.05 / Net I/σ(I): 22
Reflection shellResolution: 1.48→1.5 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1368 / CC1/2: 0.951 / Rpim(I) all: 0.154 / Rrim(I) all: 0.251 / % possible all: 76.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.5.8data scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5ev4

5ev4


Resolution: 1.48→37.76 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 13.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1573 2383 6.64 %
Rwork0.1307 33531 -
obs0.1324 35914 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.49 Å2 / Biso mean: 23.4301 Å2 / Biso min: 10.19 Å2
Refinement stepCycle: final / Resolution: 1.48→37.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 160 3 269 1925
Biso mean--32.97 31.34 -
Num. residues----207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.48-1.510.17151130.10881587170080
1.51-1.540.17191380.096919472085100
1.54-1.570.14421420.101219762118100
1.57-1.610.14831370.098319642101100
1.61-1.660.1571400.09419652105100
1.66-1.710.15461400.097119652105100
1.71-1.760.13161390.095419832122100
1.76-1.820.14231400.119742114100
1.82-1.90.13671440.105919682112100
1.9-1.980.16521390.115819912130100
1.98-2.090.17261430.116919812124100
2.09-2.220.14331420.115319942136100
2.22-2.390.15121420.120719942136100
2.39-2.630.15351400.130620162156100
2.63-3.010.18271430.141720222165100
3.01-3.790.14021460.1420452191100
3.79-37.760.17341550.166421592314100

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