Structure of human Retinal Degeneration 3(RD3) Protein

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 2.3 of the entry. See complete history


Retinal degeneration 3 (RD3) protein, a retinal guanylyl cyclase regulator, forms a monomeric and elongated four-helix bundle.

Peshenko, I.V.Yu, Q.Lim, S.Cudia, D.Dizhoor, A.M.Ames, J.B.

(2019) J Biol Chem 294: 2318-2328

  • DOI: https://doi.org/10.1074/jbc.RA118.006106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Retinal degeneration 3 (RD3) protein promotes accumulation of retinal membrane guanylyl cyclase (RetGC) in the photoreceptor outer segment and suppresses RetGC activation by guanylyl cyclase-activating proteins (GCAPs). Mutations truncating RD3 cause severe congenital blindness by preventing the inhibitory binding of RD3 to the cyclase. The high propensity of RD3 to aggregate in solution has prevented structural analysis. Here, we produced a highly soluble variant of human RD3 (residues 18-160) that is monomeric and can still bind and negatively regulate RetGC. The NMR solution structure of RD3 revealed an elongated backbone structure (70 Å long and 30 Å wide) consisting of a four-helix bundle with a long unstructured loop between helices 1 and 2. The structure reveals that RD3 residues previously implicated in the RetGC binding map to a localized and contiguous area on the structure, involving a loop between helices 2 and 3 and adjacent parts of helices 3 and 4. The NMR structure of RD3 was validated by mutagenesis. Introducing Trp 85 or Phe 29 to replace Cys or Leu, respectively, disrupts packing in the hydrophobic core and lowers RD3's apparent affinity for RetGC1. Introducing a positive charge at the interface (Glu 32 to Lys) also lowered the affinity. Conversely, introducing Val in place of Cys 93 stabilized the hydrophobic core and increased the RD3 affinity for the cyclase. The NMR structure of RD3 presented here provides a structural basis for elucidating RD3-RetGC interactions relevant for normal vision or blindness.

  • Organizational Affiliation

    From the Pennsylvania College of Optometry, Salus University, Elkins Park, Pennsylvania 19027 and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein RD3143Homo sapiensMutation(s): 1 
Gene Names: RD3C1orf36
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z3Z2 (Homo sapiens)
Explore Q7Z3Z2 
Go to UniProtKB:  Q7Z3Z2
GTEx:  ENSG00000198570 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z3Z2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesEY012347

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 2.0: 2019-02-27
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2019-12-11
    Changes: Author supporting evidence, Data collection
  • Version 2.2: 2023-06-14
    Changes: Database references, Other
  • Version 2.3: 2024-05-15
    Changes: Data collection, Database references