7MY4

Crystal Structure of the SPA17 Docking and Dimerization Domain from Danio rerio

  • Classification: PROTEIN BINDING
  • Organism(s): Danio rerio
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-05-20 Released: 2021-05-26 
  • Deposition Author(s): Dahlin, H.R., Zheng, N.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Beyond PKA: Evolutionary and structural insights that define a docking and dimerization domain superfamily.

Dahlin, H.R.Zheng, N.Scott, J.D.

(2021) J Biol Chem 297: 100927-100927

  • DOI: https://doi.org/10.1016/j.jbc.2021.100927
  • Primary Citation of Related Structures:  
    7MY4

  • PubMed Abstract: 

    Protein-interaction domains can create unique macromolecular complexes that drive evolutionary innovation. By combining bioinformatic and phylogenetic analyses with structural approaches, we have discovered that the docking and dimerization (D/D) domain of the PKA regulatory subunit is an ancient and conserved protein fold. An archetypal function of this module is to interact with A-kinase-anchoring proteins (AKAPs) that facilitate compartmentalization of this key cell-signaling enzyme. Homology searching reveals that D/D domain proteins comprise a superfamily with 18 members that function in a variety of molecular and cellular contexts. Further in silico analyses indicate that D/D domains segregate into subgroups on the basis of their similarity to type I or type II PKA regulatory subunits. The sperm autoantigenic protein 17 (SPA17) is a prototype of the type II or R2D2 subgroup that is conserved across metazoan phyla. We determined the crystal structure of an extended D/D domain from SPA17 (amino acids 1-75) at 1.72 Å resolution. This revealed a four-helix bundle-like configuration featuring terminal β-strands that can mediate higher order oligomerization. In solution, SPA17 forms both homodimers and tetramers and displays a weak affinity for AKAP18. Quantitative approaches reveal that AKAP18 binding occurs at nanomolar affinity when SPA17 heterodimerizes with the ropporin-1-like D/D protein. These findings expand the role of the D/D fold as a versatile protein-interaction element that maintains the integrity of macromolecular architectures within organelles such as motile cilia.


  • Organizational Affiliation

    Department of Pharmacology, University of Washington, Seattle, Washington, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm autoantigenic protein 17
A, B, C, D
74Danio rerioMutation(s): 0 
Gene Names: spa17
UniProt
Find proteins for F1QK17 (Danio rerio)
Explore F1QK17 
Go to UniProtKB:  F1QK17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1QK17
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.957α = 90
b = 60.957β = 90
c = 89.021γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01 DK119192

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2021-08-11
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description