3VAM

Structure of U2AF65 variant with BrU5C2 DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs.

Jenkins, J.L.Agrawal, A.A.Gupta, A.Green, M.R.Kielkopf, C.L.

(2013) Nucleic Acids Res. 41: 3859-3873

  • DOI: 10.1093/nar/gkt046
  • Primary Citation of Related Structures:  3VAF, 3VAG, 3VAH, 3VAI, 3VAJ, 3VAK, 3VAL

  • PubMed Abstract: 
  • Degenerate splice site sequences mark the intron boundaries of pre-mRNA transcripts in multicellular eukaryotes. The essential pre-mRNA splicing factor U2AF(65) is faced with the paradoxical tasks of accurately targeting polypyrimidine (Py) tracts pr ...

    Degenerate splice site sequences mark the intron boundaries of pre-mRNA transcripts in multicellular eukaryotes. The essential pre-mRNA splicing factor U2AF(65) is faced with the paradoxical tasks of accurately targeting polypyrimidine (Py) tracts preceding 3' splice sites while adapting to both cytidine and uridine nucleotides with nearly equivalent frequencies. To understand how U2AF(65) recognizes degenerate Py tracts, we determined six crystal structures of human U2AF(65) bound to cytidine-containing Py tracts. As deoxy-ribose backbones were required for co-crystallization with these Py tracts, we also determined two baseline structures of U2AF(65) bound to the deoxy-uridine counterparts and compared the original, RNA-bound structure. Local structural changes suggest that the N-terminal RNA recognition motif 1 (RRM1) is more promiscuous for cytosine-containing Py tracts than the C-terminal RRM2. These structural differences between the RRMs were reinforced by the specificities of wild-type and site-directed mutant U2AF(65) for region-dependent cytosine- and uracil-containing RNA sites. Small-angle X-ray scattering analyses further demonstrated that Py tract variations select distinct inter-RRM spacings from a pre-existing ensemble of U2AF(65) conformations. Our results highlight both local and global conformational selection as a means for universal 3' splice site recognition by U2AF(65).


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Splicing factor U2AF 65 kDa subunit
A, B
174Homo sapiensGene 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*CP*UP*UP*(BRU)P*UP*U)-3')P,E7N/A
Small Molecules
Ligands 4 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, B
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
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: 2.4 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 166.108α = 90.00
b = 37.973β = 125.49
c = 101.974γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy