6MZB

Cryo-EM structure of phosphodiesterase 6

  • Classification: SIGNALING PROTEIN
  • Organism(s): Bos taurus
  • Expression System: Bos taurus
  • Mutation(s): No 

  • Deposited: 2018-11-04 Released: 2019-03-06 
  • Deposition Author(s): Gulati, S., Palczewski, K.
  • Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Cryo-EM structure of phosphodiesterase 6 reveals insights into the allosteric regulation of type I phosphodiesterases.

Gulati, S.Palczewski, K.Engel, A.Stahlberg, H.Kovacik, L.

(2019) Sci Adv 5: eaav4322-eaav4322

  • DOI: https://doi.org/10.1126/sciadv.aav4322
  • Primary Citation of Related Structures:  
    6MZB

  • PubMed Abstract: 

    Cyclic nucleotide phosphodiesterases (PDEs) work in conjunction with adenylate/guanylate cyclases to regulate the key second messengers of G protein-coupled receptor signaling. Previous attempts to determine the full-length structure of PDE family members at high-resolution have been hindered by structural flexibility, especially in their linker regions and N- and C-terminal ends. Therefore, most structure-activity relationship studies have so far focused on truncated and conserved catalytic domains rather than the regulatory domains that allosterically govern the activity of most PDEs. Here, we used single-particle cryo-electron microscopy to determine the structure of the full-length PDE6αβ2γ complex. The final density map resolved at 3.4 Å reveals several previously unseen structural features, including a coiled N-terminal domain and the interface of PDE6γ subunits with the PDE6αβ heterodimer. Comparison of the PDE6αβ2γ complex with the closed state of PDE2A sheds light on the conformational changes associated with the allosteric activation of type I PDEs.


  • Organizational Affiliation

    Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, 829 Health Sciences Road, Irvine, CA 92617, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit betaA [auth B]853Bos taurusMutation(s): 0 
Gene Names: PDE6BPDEB
EC: 3.1.4.35
UniProt
Find proteins for P23439 (Bos taurus)
Explore P23439 
Go to UniProtKB:  P23439
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23439
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alphaB [auth A]859Bos taurusMutation(s): 0 
Gene Names: PDE6APDEA
EC: 3.1.4.35
UniProt
Find proteins for P11541 (Bos taurus)
Explore P11541 
Go to UniProtKB:  P11541
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11541
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
C, D
87Bos taurusMutation(s): 0 
Gene Names: PDE6GPDEG
EC: 3.1.4.35
UniProt
Find proteins for P04972 (Bos taurus)
Explore P04972 
Go to UniProtKB:  P04972
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04972
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesEY009339
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesEY027283
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesEY024864

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 2.0: 2021-05-19
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2024-10-09
    Changes: Data collection, Database references, Structure summary