4TU8

STRUCTURE OF U2AF65 VARIANT WITH BRU5A6 DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


This is version 1.6 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 U S A 111: 17420-17425

  • DOI: https://doi.org/10.1073/pnas.1412743111
  • Primary Citation of Related Structures:  
    4TU7, 4TU8, 4TU9

  • 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 found that neurofibromatosis- or retinitis pigmentosa-causing mutations in the 5' regions of Py tracts severely reduce U2AF(65) affinity ...

    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 clara_kielkopf@urmc.rochester.edu.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor U2AF 65 kDa subunit
A, B
174Homo sapiensMutation(s): 0 
Gene Names: U2AF2, U2AF65
UniProt & NIH Common Fund Data Resources
Find proteins for P26368 (Homo sapiens)
Explore P26368 
Go to UniProtKB:  P26368
PHAROS:  P26368
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26368
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*UP*UP*UP*UP*(BRU)P*DA*U)-3')C [auth P],
D [auth E]		7Homo sapiens
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPQ
Query on CPQ
Download Ideal Coordinates CCD File 
T [auth B]N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE
C42 H75 N3 O15
OJSUWTDDXLCUFR-HGZMBBKESA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
Y [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
DIO
Query on DIO
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
O [auth B]
P [auth B]
Q [auth B]
E [auth A],
F [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.04α = 90
b = 37.178β = 125.66
c = 100.71γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM070503
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesRR026501

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Derived calculations
  • Version 1.2: 2014-12-10
    Changes: Database references
  • Version 1.3: 2014-12-24
    Changes: Database references
  • Version 1.4: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.5: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.6: 2022-03-23
    Changes: Author supporting evidence, Database references