Biological Assembly 1  

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

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 24.74 kDa 
• Atom Count: 1,862 
• Modelled Residue Count: 204 
• Deposited Residue Count: 212 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 6XLX

Crystal structure of cancer-associated G301D mutant of U2AF65 bound to AdML splice site

• PDB DOI: 10.2210/pdb6XLX/pdb
• NDB: 6XLX

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


• Deposited: 2020-06-29 Released: 2020-10-07 
• Deposition Author(s): Maji, D., 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: 1.70 Å
• R-Value Free: 0.194 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing.

Maji, D., Glasser, E., Henderson, S., Galardi, J., Pulvino, M.J., Jenkins, J.L., Kielkopf, C.L.

(2020) J Biol Chem 295: 17148-17157

• PubMed: 33020180 
• DOI: 10.1074/jbc.RA120.015339
• Primary Citation of Related Structures:  
  6XLV, 6XLW, 6XLX


• PubMed Abstract: 
  

High-throughput sequencing of hematologic malignancies and other cancers has revealed recurrent mis-sense mutations of genes encoding pre-mRNA splicing factors. The essential splicing factor U2AF2 recognizes a polypyrimidine-tract splice-site signal and initiates spliceosome assembly. Here, we investigate representative, acquired U2AF2 mutations, namely N196K or G301D amino acid substitutions associated with leukemia or solid tumors, respectively. We determined crystal structures of the wild-type (WT) compared with N196K- or G301D-substituted U2AF2 proteins, each bound to a prototypical AdML polypyrimidine tract, at 1.5, 1.4, or 1.7 Å resolutions. The N196K residue appears to stabilize the open conformation of U2AF2 with an inter-RNA recognition motif hydrogen bond, in agreement with an increased apparent RNA-binding affinity of the N196K-substituted protein. The G301D residue remains in a similar position as the WT residue, where unfavorable proximity to the RNA phosphodiester could explain the decreased RNA-binding affinity of the G301D-substituted protein. We found that expression of the G301D-substituted U2AF2 protein reduces splicing of a minigene transcript carrying prototypical splice sites. We further show that expression of either N196K- or G301D-substituted U2AF2 can subtly alter splicing of representative endogenous transcripts, despite the presence of endogenous, WT U2AF2 such as would be present in cancer cells. Altogether, our results demonstrate that acquired U2AF2 mutations such as N196K and G301D are capable of dysregulating gene expression for neoplastic transformation.

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Organizational Affiliation: 

Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor U2AF 65 kDa subunit	A	204	Homo sapiens	Mutation(s): 1  Gene Names: U2AF2, U2AF65
UniProt & NIH Common Fund Data Resources
Find proteins for P26368 (Homo sapiens) Explore P26368  Go to UniProtKB:  P26368
PHAROS:  P26368

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.194 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.492	α = 90
b = 61.875	β = 90
c = 77.421	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Maji, D., 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	GM070503-15

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references