7C08

Crystal structure of S34Y mutant of yeast U2AF1 complex bound to 3' splice site RNA, 5'-UAGGU.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1.

Yoshida, H., Park, S.Y., Sakashita, G., Nariai, Y., Kuwasako, K., Muto, Y., Urano, T., Obayashi, E.

(2020) Nat Commun 11: 4744-4744

  • DOI: https://doi.org/10.1038/s41467-020-18559-6
  • Primary Citation of Related Structures:  
    7C06, 7C07, 7C08

  • PubMed Abstract: 

    • The accurate exclusion of introns by RNA splicing is critical for the production of mature mRNA. U2AF1 binds specifically to the 3´ splice site, which includes an essential AG dinucleotide. Even a single amino acid mutation of U2AF1 can cause serious disease such as certain cancers or myelodysplastic syndromes ...

    The accurate exclusion of introns by RNA splicing is critical for the production of mature mRNA. U2AF1 binds specifically to the 3´ splice site, which includes an essential AG dinucleotide. Even a single amino acid mutation of U2AF1 can cause serious disease such as certain cancers or myelodysplastic syndromes. Here, we describe the first crystal structures of wild-type and pathogenic mutant U2AF1 complexed with target RNA, revealing the mechanism of 3´ splice site selection, and how aberrant splicing results from clinically important mutations. Unexpected features of this mechanism may assist the future development of new treatments against diseases caused by splicing errors.

    Organizational Affiliation: 

    Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, 693-8501, Japan. eijioba@med.shimane-u.ac.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor U2AF 23 kDa subunit
A, D, G, J, M, P, S, V, Y
A, D, G, J, M, P, S, V, Y
216Schizosaccharomyces pombe 972h-Mutation(s): 1 
Gene Names: SPAP8A3.06
UniProt
Find proteins for Q09176 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q09176 
Go to UniProtKB:  Q09176
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09176
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor U2AF 59 kDa subunit
B, E, H, K, N, Q, T, W, Z
B, E, H, K, N, Q, T, W, Z
69Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp2, mis11, SPBC146.07
UniProt
Find proteins for P36629 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P36629 
Go to UniProtKB:  P36629
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UniProt GroupP36629
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
AA [auth 1],
C,
F,
I,
L,
O,
R,
U,
X
6synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
BA [auth A],
CA [auth A],
DA [auth D],
EA [auth D],
FA [auth G],
BA [auth A],
CA [auth A],
DA [auth D],
EA [auth D],
FA [auth G],
GA [auth G],
HA [auth J],
IA [auth J],
JA [auth M],
KA [auth M],
LA [auth P],
MA [auth P],
NA [auth S],
OA [auth S],
PA [auth V],
QA [auth V],
RA [auth Y],
SA [auth Y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.506α = 90
b = 259β = 100.681
c = 94.822γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18K06086

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references