5EV2

Structure II of Intact U2AF65 Recognizing the 3' Splice Site Signal

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal.

Agrawal, A.A., Salsi, E., Chatrikhi, R., Henderson, S., Jenkins, J.L., Green, M.R., Ermolenko, D.N., Kielkopf, C.L.

(2016) Nat Commun 7: 10950-10950

  • DOI: 10.1038/ncomms10950
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • How the essential pre-mRNA splicing factor U2AF(65) recognizes the polypyrimidine (Py) signals of the major class of 3' splice sites in human gene transcripts remains incompletely understood. We determined four structures of an extended U2AF(65)-RNA- ...

    How the essential pre-mRNA splicing factor U2AF(65) recognizes the polypyrimidine (Py) signals of the major class of 3' splice sites in human gene transcripts remains incompletely understood. We determined four structures of an extended U2AF(65)-RNA-binding domain bound to Py-tract oligonucleotides at resolutions between 2.0 and 1.5 Å. These structures together with RNA binding and splicing assays reveal unforeseen roles for U2AF(65) inter-domain residues in recognizing a contiguous, nine-nucleotide Py tract. The U2AF(65) linker residues between the dual RNA recognition motifs (RRMs) recognize the central nucleotide, whereas the N- and C-terminal RRM extensions recognize the 3' terminus and third nucleotide. Single-molecule FRET experiments suggest that conformational selection and induced fit of the U2AF(65) RRMs are complementary mechanisms for Py-tract association. Altogether, these results advance the mechanistic understanding of molecular recognition for a major class of splice site signals.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Splicing factor U2AF 65 kDa subunit
A
201Homo 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'-R(P*UP*U)-D(P*UP*U)-R(P*U)-D(P*UP*(BRU)P*U)-3')B8synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE
Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO
Download SDF File 
Download CCD File 
A
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG
Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
B
DNA LINKINGC9 H12 Br N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.151 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 61.469α = 90.00
b = 115.220β = 90.00
c = 59.544γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM070503

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Derived calculations