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- PDB-7s3c: Crystal structure of intact U2AF65 RRM-region bound to AdML-A5 ol... -

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Basic information

Entry
Database: PDB / ID: 7s3c
TitleCrystal structure of intact U2AF65 RRM-region bound to AdML-A5 oligonucleotide
Components
  • DNA/RNA (5'-R(P*UP*UP*(UD)P*AP*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: 1.51 Å
AuthorsGlasser, E. / 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)GM070503-15 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: Polymer sequence / Category: entity_poly / Item: _entity_poly.type
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,7102
Polymers24,7102
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-11 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.549, 55.771, 76.414
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*AP*U)-D(P*(BRU))-R(P*CP*C)-3')


Mass: 2472.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 1.9 Å3/Da / Density % sol: 35.31 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.24 M malonate, 26% Peg 3350, 10% sucrose, LDAO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2016
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: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.51→38.21 Å / Num. obs: 54400 / % possible obs: 97.7 % / Redundancy: 6.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.031 / Net I/σ(I): 14.8
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3555 / CC1/2: 0.768 / Rpim(I) all: 0.432 / % possible all: 64

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimless0.5.27data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5ev4

5ev4


Resolution: 1.51→37.84 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 18.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1902 3631 6.67 %
Rwork0.1585 50769 -
obs0.1607 54400 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.29 Å2 / Biso mean: 33.8964 Å2 / Biso min: 14.94 Å2
Refinement stepCycle: final / Resolution: 1.51→37.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 162 0 200 1819
Biso mean---39.42 -
Num. residues----199
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.51-1.530.256840.2527992107650
1.53-1.560.27511130.23391898201193
1.56-1.580.27841440.19821985212998
1.58-1.60.24391640.19141948211299
1.6-1.630.19111450.185620102155100
1.63-1.650.20721460.16791982212899
1.65-1.680.22381340.17432003213799
1.68-1.710.23361490.16281994214399
1.71-1.740.24541630.17481957212099
1.74-1.780.23571300.16971981211199
1.78-1.820.23831180.15352045216399
1.82-1.860.18121340.15520072141100
1.86-1.910.17921870.14491929211699
1.91-1.960.2181510.14742009216099
1.96-2.020.20761160.143120072123100
2.02-2.080.17691180.13862040215899
2.08-2.160.17731300.13761996212699
2.16-2.240.21441420.143319892131100
2.24-2.340.21441400.143820012141100
2.34-2.470.19051490.15231991214099
2.47-2.620.19531730.15741985215899
2.62-2.820.18281300.161120152145100
2.83-3.110.18371330.161320152148100
3.11-3.560.15571540.149519892143100
3.56-4.480.18211450.14241998214399
4.48-37.840.18291390.19120032142100

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