5EV3 | pdb_00005ev3

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

• PDB DOI: https://doi.org/10.2210/pdb5EV3/pdb
• NAKB: 5EV3

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-11-19 Released: 2016-02-24 
• Deposition Author(s): Agrawal, A.A., Jenkins, J.L., Kielkopf, C.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.186 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

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

• PubMed: 26952537 
• DOI: https://doi.org/10.1038/ncomms10950
• Primary Citation Related Structures: 
  5EV1, 5EV2, 5EV3, 5EV4


• 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-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.

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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.
Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.39 kDa 
• Atom Count: 1,921 
• Modeled Residue Count: 204 
• Deposited Residue Count: 209 
• Unique protein chains: 1
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor U2AF 65 kDa subunit	A	201	Homo sapiens	Mutation(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 GTEx:  ENSG00000063244

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(P*UP*U)-D(P*U)-R(P*UP*U)-D(P*(BRU)P*UP*U)-3')	B	8	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.186 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.351	α = 90
b = 62.196	β = 90
c = 77.425	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-02-24 
Deposition Author(s): Agrawal, A.A., Jenkins, J.L., Kielkopf, C.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM070503

Revision History  

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2016-03-23
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2024-03-06
  Changes: Data collection, Database references