Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 24717.67 
• Atom Count: 1711 
• Residue Count: 209 
• Unique protein chains: 1
• Unique hybrid chains: 1

5EV2

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

• DOI: 10.2210/pdb5EV2/pdb
• NDB: 5EV2

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli BL21


• 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: 1.86 Å
• R-Value Free: 0.188 
• R-Value Work: 0.151 

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: 10.1038/ncomms10950
• Primary Citation of Related Structures:  
  5EV4, 5EV3, 5EV1


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Splicing factor U2AF 65 kDa subunit	A	201	Homo sapiens	Mutation(s): 0  Gene Names: U2AF2 (U2AF65)
Find proteins for P26368 (Homo sapiens) Go to Gene View: U2AF2 Go to UniProtKB:  P26368

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PGE	A	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
DIO	A	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N
PEG	A	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BRU	B	DNA LINKING	C9 H12 Br N2 O8 P		DU

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 = 61.469	α = 90.00
b = 115.220	β = 90.00
c = 59.544	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-11-19 
• 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
  Type: Database references
• Version 1.2: 2017-09-27
  Type: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Type: Author supporting evidence