7EG4

Cryo-EM structure of nauclefine-induced PDE3A-SLFN12 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of PDE3A-SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells.

Chen, J.Liu, N.Huang, Y.Wang, Y.Sun, Y.Wu, Q.Li, D.Gao, S.Wang, H.W.Huang, N.Qi, X.Wang, X.

(2021) Nat Commun 12: 6204-6204

  • DOI: https://doi.org/10.1038/s41467-021-26546-8
  • Primary Citation of Related Structures:  
    7EG0, 7EG1, 7EG4

  • PubMed Abstract: 

    Molecular glues are a class of small molecular drugs that mediate protein-protein interactions, that induce either the degradation or stabilization of target protein. A structurally diverse group of chemicals, including 17-β-estradiol (E2), anagrelide, nauclefine, and DNMDP, induces apoptosis by forming complexes with phosphodiesterase 3A (PDE3A) and Schlafen 12 protein (SLFN12). They do so by binding to the PDE3A enzymatic pocket that allows the compound-bound PDE3A to recruit and stabilize SLFN12, which in turn blocks protein translation, leading to apoptosis. In this work, we report the high-resolution cryo-electron microscopy structure of PDE3A-SLFN12 complexes isolated from cultured HeLa cells pre-treated with either anagrelide, or nauclefine, or DNMDP. The PDE3A-SLFN12 complexes exhibit a butterfly-like shape, forming a heterotetramer with these small molecules, which are packed in a shallow pocket in the catalytic domain of PDE3A. The resulting small molecule-modified interface binds to the short helix (E552-I558) of SLFN12 through hydrophobic interactions, thus "gluing" the two proteins together. Based on the complex structure, we designed and synthesized analogs of anagrelide, a known drug used for the treatment of thrombocytosis, to enhance their interactions with SLFN12, and achieved superior efficacy in inducing apoptosis in cultured cells as well as in tumor xenografts.


  • Organizational Affiliation

    National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP-inhibited 3',5'-cyclic phosphodiesterase AA [auth C],
C [auth A]
434Homo sapiensMutation(s): 0 
Gene Names: PDE3A
EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q14432 (Homo sapiens)
Explore Q14432 
Go to UniProtKB:  Q14432
PHAROS:  Q14432
GTEx:  ENSG00000172572 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14432
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Schlafen family member 12B [auth D],
D [auth B]
567Homo sapiensMutation(s): 3 
Gene Names: SLFN12
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYM2 (Homo sapiens)
Explore Q8IYM2 
Go to UniProtKB:  Q8IYM2
PHAROS:  Q8IYM2
GTEx:  ENSG00000172123 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IYM2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J36
Query on J36

Download Ideal Coordinates CCD File 
E [auth C],
I [auth A]
Parvine
C18 H13 N3 O
BGFQUYBVDVRJSP-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth D],
L [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth C],
G [auth C],
J [auth A],
K [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references