4TU8

STRUCTURE OF U2AF65 VARIANT WITH BRU5A6 DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.918 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure-guided U2AF65 variant improves recognition and splicing of a defective pre-mRNA.

Agrawal, A.A.McLaughlin, K.J.Jenkins, J.L.Kielkopf, C.L.

(2014) Proc.Natl.Acad.Sci.USA 111: 17420-17425

  • DOI: 10.1073/pnas.1412743111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Purine interruptions of polypyrimidine (Py) tract splice site signals contribute to human genetic diseases. The essential splicing factor U2AF(65) normally recognizes a Py tract consensus sequence preceding the major class of 3' splice sites. We foun ...

    Purine interruptions of polypyrimidine (Py) tract splice site signals contribute to human genetic diseases. The essential splicing factor U2AF(65) normally recognizes a Py tract consensus sequence preceding the major class of 3' splice sites. We found that neurofibromatosis- or retinitis pigmentosa-causing mutations in the 5' regions of Py tracts severely reduce U2AF(65) affinity. Conversely, we identified a preferred binding site of U2AF(65) for purine substitutions in the 3' regions of Py tracts. Based on a comparison of new U2AF(65) structures bound to either A- or G-containing Py tracts with previously identified pyrimidine-containing structures, we expected to find that a D231V amino acid change in U2AF(65) would specify U over other nucleotides. We found that the crystal structure of the U2AF(65)-D231V variant confirms favorable packing between the engineered valine and a target uracil base. The D231V amino acid change restores U2AF(65) affinity for two mutated splice sites that cause human genetic diseases and successfully promotes splicing of a defective retinitis pigmentosa-causing transcript. We conclude that reduced U2AF(65) binding is a molecular consequence of disease-relevant mutations, and that a structure-guided U2AF(65) variant is capable of manipulating gene expression in eukaryotic cells.


    Organizational Affiliation

    Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Splicing factor U2AF 65 kDa subunit
A, B
174Homo sapiensMutation(s): 0 
Gene Names: U2AF2 (U2AF65)
Find proteins for P26368 (Homo sapiens)
Go to Gene View: U2AF2
Go to UniProtKB:  P26368
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*UP*UP*UP*UP*(BRU)P*DA*U)-3')P,E7Homo sapiens
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CPQ
Query on CPQ

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B
N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE
DEOXY-BIGCHAP
C42 H75 N3 O15
OJSUWTDDXLCUFR-HGZMBBKESA-N
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

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A, B
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
E, P
DNA LINKINGC9 H12 Br N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.918 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 164.040α = 90.00
b = 37.178β = 125.66
c = 100.710γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
DENZOdata reduction
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Derived calculations
  • Version 1.2: 2014-12-10
    Type: Database references
  • Version 1.3: 2014-12-24
    Type: Database references
  • Version 1.4: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy