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- PDB-5w0h: Structure of U2AF65 (U2AF2) RRM2 at 1.11 Angstrom Resolution -

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Basic information

Entry
Database: PDB / ID: 5w0h
TitleStructure of U2AF65 (U2AF2) RRM2 at 1.11 Angstrom Resolution
ComponentsSplicing factor U2AF 65 kDa subunit
KeywordsRNA BINDING PROTEIN/RNA / RNA SPLICING FACTOR / RNA RECOGNITION MOTIF / 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 / 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
Splicing factor U2AF 65 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.11 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 / Category: database_2 / pdbx_audit_support
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
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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)8,9661
Polymers8,9661
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.430, 38.203, 72.722
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: 8966.237 Da / Num. of mol.: 1 / Fragment: RNA Recognition Motif 2 (RRM2), residues 258-336
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 26% (w/v) PEG 8000, 0.1 M NaOAc, 0.2 mM TCEP, 10% (v/v) dioxane, 0.2 ul BigCHAP, 0.05 M potassium phosphate monobasic

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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: 1.11→20.69 Å / Num. obs: 36104 / % possible obs: 97.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 11.44 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 27.8
Reflection shellResolution: 1.11→1.13 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.5 / % possible all: 92.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G4B RRM2

2g4b


Resolution: 1.11→20.69 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.32
RfactorNum. reflection% reflection
Rfree0.1681 1938 5.37 %
Rwork0.1528 --
obs0.1537 36085 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.74 Å2 / Biso mean: 18.5012 Å2 / Biso min: 7.31 Å2
Refinement stepCycle: final / Resolution: 1.11→20.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms608 0 0 141 749
Biso mean---36.14 -
Num. residues----80
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007733
X-RAY DIFFRACTIONf_angle_d0.885999
X-RAY DIFFRACTIONf_chiral_restr0.078110
X-RAY DIFFRACTIONf_plane_restr0.007134
X-RAY DIFFRACTIONf_dihedral_angle_d15.828289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1126-1.14040.22181200.20272137225787
1.1404-1.17120.15411350.15542368250396
1.1712-1.20570.15291370.1322416255396
1.2057-1.24460.20571390.13252423256297
1.2446-1.28910.13951380.12762420255897
1.2891-1.34070.18621400.13292439257998
1.3407-1.40170.13871360.12042465260199
1.4017-1.47560.17361400.12122482262299
1.4756-1.5680.14771420.112824942636100
1.568-1.6890.12981440.112125242668100
1.689-1.85890.161440.135925332677100
1.8589-2.12760.13831230.14532177230086
2.1276-2.67970.18181460.174725732719100
2.6797-20.69220.18281540.175426962850100

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