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- PDB-6xlw: Crystal structure of U2AF65 bound to AdML splice site sequence -

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Basic information

Entry
Database: PDB / ID: 6xlw
TitleCrystal structure of U2AF65 bound to AdML splice site sequence
Components
  • DNA/RNA (5'-R(P*UP*UP*(UD)P*UP*U)-D(P*(BRU))-R(P*CP*C)-3')
  • Splicing factor U2AF 65 kDa subunit
KeywordsRNA BINDING PROTEIN/SPLICING / PROTEIN-RNA COMPLEX / RNA SPLICING FACTOR / RNA RECOGNITION MOTIF / POLYPYRIMIDINE TRACT / RNA BINDING PROTEIN-RNA COMPLEX / RNA BINDING PROTEIN / RNA BINDING PROTEIN-SPLICING 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 / Protein hydroxylation / spliceosomal complex assembly / negative regulation of mRNA splicing, via spliceosome / negative regulation of protein ubiquitination / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / 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 / RNA / Splicing factor U2AF 65 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsMaji, D. / 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: J.Biol.Chem. / Year: 2020
Title: Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing.
Authors: Maji, D. / Glasser, E. / Henderson, S. / Galardi, J. / Pulvino, M.J. / Jenkins, J.L. / Kielkopf, C.L.
History
DepositionJun 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Mar 16, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_src_gen / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conn
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.version
Description: Model completeness
Details: We realized that two waters in the structure should be sodium ions based on their interactions.
Provider: author / Type: Coordinate replacement
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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*UP*U)-D(P*(BRU))-R(P*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9778
Polymers24,6872
Non-polymers2906
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-55 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.398, 62.731, 77.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 2449.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 265 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1M Succinic Acid, 0.1M HEPES pH 7, 3% 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, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.5→38.71 Å / Num. obs: 33522 / % possible obs: 97 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.032 / Net I/σ(I): 22.3
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 6 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 9.9 / Num. unique obs: 1417 / CC1/2: 0.991 / Rpim(I) all: 0.062 / % possible all: 85

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless0.5.8data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→38.71 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 12.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1535 2223 6.63 %
Rwork0.1311 31299 -
obs0.1326 33522 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.71 Å2 / Biso mean: 23.3784 Å2 / Biso min: 8.95 Å2
Refinement stepCycle: final / Resolution: 1.5→38.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 160 34 264 1964
Biso mean--36.46 30.78 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081787
X-RAY DIFFRACTIONf_angle_d1.0382461
X-RAY DIFFRACTIONf_dihedral_angle_d14.175708
X-RAY DIFFRACTIONf_chiral_restr0.072281
X-RAY DIFFRACTIONf_plane_restr0.007298
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.530.14641170.10181727184486
1.53-1.570.14021430.09671892203596
1.57-1.610.11671350.08971954208997
1.61-1.650.12231370.08811905204297
1.65-1.70.1361460.09591934208097
1.7-1.750.13971330.10591908204196
1.75-1.820.14761400.10421960210098
1.82-1.890.1441350.10641957209297
1.89-1.970.1461400.11461973211398
1.98-2.080.15961370.11581914205196
2.08-2.210.14631370.11611979211699
2.21-2.380.1551450.11841997214298
2.38-2.620.14571380.13171982212098
2.62-30.16141460.14212009215599
3-3.780.14851410.14132066220799
3.78-38.710.17781530.16872142229598

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