Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.11 kDa 
• Atom Count: 1519 
• Residue Count: 179 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2G4B

Structure of U2AF65 variant with polyuridine tract

• DOI: 10.2210/pdb2G4B/pdb
• NDB: PR0195

• Classification: RNA Binding Protein/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-02-21 Released: 2006-07-25 
• Deposition Author(s): Sickmier, E.A., Kielkopf, C.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.276 
• R-Value Work: 0.261 
• R-Value Observed: 0.262 

Literature

Structural basis of polypyrimidine tract recognition by the essential splicing factor U2AF65.

Sickmier, E.A., Frato, K.E., Paranawithana, S., Shen, H., Green, M.R., Kielkopf, C.L.

(2006) Mol Cell 23: 49-59

• PubMed: 16818232 
• DOI: 10.1016/j.molcel.2006.05.025
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The essential pre-mRNA splicing factor, U2AF(65), guides the early stages of splice site choice by recognizing a polypyrimidine (Py) tract consensus sequence near the 3' splice site. Since Py tracts are relatively poorly conserved in higher eukaryotes, U2AF(65) is faced with the problem of specifying uridine-rich sequences, yet tolerating a variety of nucleotide substitutions found in natural Py tracts. To better understand these apparently contradictory RNA binding characteristics, the X-ray structure of the U2AF(65) RNA binding domain bound to a Py tract composed of seven uridines has been determined at 2.5 A resolution. Specific hydrogen bonds between U2AF(65) and the uracil bases provide an explanation for polyuridine recognition. Flexible side chains and bound water molecules form the majority of the base contacts and potentially could rearrange when the U2AF(65) structure adapts to different Py tract sequences. The energetic importance of conserved residues for Py tract binding is established by analysis of site-directed mutant U2AF(65) proteins using surface plasmon resonance.

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Related Citations: 

• Crystallization and preliminary X-ray analysis of a U2AF65 variant in complex with a polypyrimidine-tract analogue by use of protein engineering.
  Sickmier, E.A., Frato, K.E., Kielkopf, C.L.
  (2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 457

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Splicing factor U2AF 65 kDa subunit	A	172	Homo sapiens	Mutation(s): 0  Gene Names: U2AF65
Find proteins for P26368 (Homo sapiens) Go to UniProtKB:  P26368
NIH Common Fund Data Resources
PHAROS  P26368 GTEx  ENSG00000063244

Entity ID: 1
Molecule	Chains	Length	Organism
5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'	B	7	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIO	A	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
RNA	Kd :  1800   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.276 
• R-Value Work: 0.261 
• R-Value Observed: 0.262 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.388	α = 90
b = 129.388	β = 90
c = 62.645	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-21 
• Released Date: 2006-07-25 
Deposition Author(s): Sickmier, E.A., Kielkopf, C.L.

Revision History 

• Version 1.0: 2006-07-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.4: 2018-01-31
  Changes: Database references