Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44322.46 
• Atom Count: 2995 
• Residue Count: 362 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

3VAF

Structure of U2AF65 variant with BrU3 DNA

• DOI: 10.2210/pdb3VAF/pdb
• NDB: NA1506

• Classification: RNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2011-12-29 Released: 2013-02-13 
• Deposition Author(s): Jenkins, J.L., Kielkopf, C.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.289 
• R-Value Work: 0.231 

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

• PubMed: 23376934 
• DOI: 10.1093/nar/gkt046
• Primary Citation of Related Structures:  
  3VAM, 3VAL, 3VAK, 3VAJ, 3VAI, 3VAH, 3VAG


• 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 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).

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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, NY 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, B	174	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'-D(*UP*UP*(BRU)P*(BRU)P*UP*UP*U)-3'	P,E	7	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B, P	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CPQ	B	N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE DEOXY-BIGCHAP C42 H75 N3 O15 OJSUWTDDXLCUFR-HGZMBBKESA-N
DIO	A, B	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.289 
• R-Value Work: 0.231 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 164.296	α = 90.00
b = 36.981	β = 125.67
c = 99.431	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
PHASER	phasing
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-29 
• Released Date: 2013-02-13 
• Deposition Author(s): Jenkins, J.L., Kielkopf, C.L.

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