7LRE

Cryo-EM of the SLFN12-PDE3A complex: SLFN12 body refinement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 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 reveals requirements for activation of SLFN12 RNase.

Garvie, C.W.Wu, X.Papanastasiou, M.Lee, S.Fuller, J.Schnitzler, G.R.Horner, S.W.Baker, A.Zhang, T.Mullahoo, J.P.Westlake, L.Hoyt, S.H.Toetzl, M.Ranaghan, M.J.de Waal, L.McGaunn, J.Kaplan, B.Piccioni, F.Yang, X.Lange, M.Tersteegen, A.Raymond, D.Lewis, T.A.Carr, S.A.Cherniack, A.D.Lemke, C.T.Meyerson, M.Greulich, H.

(2021) Nat Commun 12: 4375-4375

  • DOI: 10.1038/s41467-021-24495-w
  • Primary Citation of Related Structures:  
    7LRE, 7LRC, 7LRD, 7L27, 7L28, 7L29, 7KWE

  • PubMed Abstract: 
  • DNMDP and related compounds, or velcrins, induce complex formation between the phosphodiesterase PDE3A and the SLFN12 protein, leading to a cytotoxic response in cancer cells that express elevated levels of both proteins. The mechanisms by which velcrins induce complex formation, and how the PDE3A-SLFN12 complex causes cancer cell death, are not fully understood ...

    DNMDP and related compounds, or velcrins, induce complex formation between the phosphodiesterase PDE3A and the SLFN12 protein, leading to a cytotoxic response in cancer cells that express elevated levels of both proteins. The mechanisms by which velcrins induce complex formation, and how the PDE3A-SLFN12 complex causes cancer cell death, are not fully understood. Here, we show that PDE3A and SLFN12 form a heterotetramer stabilized by binding of DNMDP. Interactions between the C-terminal alpha helix of SLFN12 and residues near the active site of PDE3A are required for complex formation, and are further stabilized by interactions between SLFN12 and DNMDP. Moreover, we demonstrate that SLFN12 is an RNase, that PDE3A binding increases SLFN12 RNase activity, and that SLFN12 RNase activity is required for DNMDP response. This new mechanistic understanding will facilitate development of velcrin compounds into new cancer therapies.


    Organizational Affiliation

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. heidig@broadinstitute.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Schlafen family member 12A, B583Homo sapiensMutation(s): 0 
Gene Names: SLFN12
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYM2 (Homo sapiens)
Explore Q8IYM2 
Go to UniProtKB:  Q8IYM2
PHAROS:  Q8IYM2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 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: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references