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- PDB-5w0g: Structure of U2AF65 (U2AF2) RRM1 at 1.07 resolution -

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Basic information

Entry
Database: PDB / ID: 5w0g
TitleStructure of U2AF65 (U2AF2) RRM1 at 1.07 resolution
ComponentsSplicing factor U2AF 65 kDa subunit
KeywordsRNA BINDING PROTEIN/RNA / RNA SPLICING FACTOR / RNA RECOGNITION MOTIF / RRM / POLYPYRIMIDINE TRACT / RNA BINDING PROTEIN / 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 processing / mRNA splicing, via spliceosome / 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
Chem-1PG / ACETATE ION / Splicing factor U2AF 65 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.07 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: Biochemistry / Year: 2017
Title: Cancer-Associated Mutations Mapped on High-Resolution Structures of the U2AF2 RNA Recognition Motifs.
Authors: Glasser, E. / Agrawal, A.A. / Jenkins, J.L. / Kielkopf, C.L.
History
DepositionMay 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_symmetry
Revision 1.2Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Splicing factor U2AF 65 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0725
Polymers9,6301
Non-polymers4424
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-38 kcal/mol
Surface area5050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.707, 28.707, 185.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

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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: 9629.989 Da / Num. of mol.: 1 / Fragment: RNA RECOGNITION motif 1 (RRM1), residues 148-229
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.13 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 21% (w/v) PEG MME 550, 210 mM zinc acetate, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9779 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.07→16.98 Å / Num. obs: 33973 / % possible obs: 94.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 12.39 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.3
Reflection shellResolution: 1.07→1.09 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.9 / % possible all: 67.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2HZC

2hzc


Resolution: 1.07→16.98 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 13.07
RfactorNum. reflection% reflection
Rfree0.153 1876 5.66 %
Rwork0.135 --
obs0.136 33138 92.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.03 Å2
Refinement stepCycle: LAST / Resolution: 1.07→16.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms652 0 23 132 807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023742
X-RAY DIFFRACTIONf_angle_d1.393985
X-RAY DIFFRACTIONf_dihedral_angle_d16.871283
X-RAY DIFFRACTIONf_chiral_restr0.086103
X-RAY DIFFRACTIONf_plane_restr0.008133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.071-1.10.2186920.19041611X-RAY DIFFRACTION64
1.1-1.13230.18331310.15162179X-RAY DIFFRACTION87
1.1323-1.16890.16971380.12622379X-RAY DIFFRACTION94
1.1689-1.21060.16721480.12372457X-RAY DIFFRACTION96
1.2106-1.25910.1611530.1242476X-RAY DIFFRACTION97
1.2591-1.31640.14141530.11052502X-RAY DIFFRACTION98
1.3164-1.38570.15731520.11082519X-RAY DIFFRACTION99
1.3857-1.47250.12211530.10742535X-RAY DIFFRACTION99
1.4725-1.58610.12551520.1062588X-RAY DIFFRACTION99
1.5861-1.74560.12331480.10982578X-RAY DIFFRACTION99
1.7456-1.99790.13541720.11612566X-RAY DIFFRACTION98
1.9979-2.51580.14711470.12682575X-RAY DIFFRACTION95
2.5158-16.98020.18111370.17712297X-RAY DIFFRACTION79

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