9FRX | pdb_00009frx

Porcine Retinol-Binding Protein 3 (RBP3)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 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

CryoEM structure and small-angle X-ray scattering analyses of porcine retinol-binding protein 3.

Kaushik, V.Gessa, L.Kumar, N.Pinkas, M.Czarnocki-Cieciura, M.Palczewski, K.Novacek, J.Fernandes, H.

(2025) Open Biol 15: 240180-240180

  • DOI: https://doi.org/10.1098/rsob.240180
  • Primary Citation of Related Structures:  
    9FRX

  • PubMed Abstract: 

    The vertebrate visual cycle hinges on enzymatically converting all- trans -retinol (at-ROL) into 11- cis -retinal (11c-RAL), the chromophore that binds to opsins in photoreceptors, forming light-responsive pigments. When struck by a photon, these pigments activate the phototransduction pathway and initiate the process of vision. The enzymatic isomerization of at-ROL, crucial for restoring the visual pigments and preparing them to receive new light stimuli, relies on various enzymes found in both the photoreceptors and retinal pigment epithelium cells. To function effectively, retinoids must shuttle between these two cell types. Retinol-binding protein 3 (RBP3), located in the interphotoreceptor matrix, probably plays a pivotal role in this transport mechanism. Comprised of four retinoid-binding modules, RBP3 also binds fatty acids, potentially aiding retinal function by facilitating the loading and unloading of different retinoids at specific cell types thereby directing the cycle. In this study, we present a 3.67 Å cryoEM structure of porcine RBP3, along with molecular docking analysis and corroborative in-solution small-angle X-ray scattering data for titration of RBP3 with relevant ligands, that also give insights on RBP3 conformational adaptability.


  • Organizational Affiliation
    • Institute of Physical Chemistry, Polish Academy of Sciences , Warsaw, Poland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinol binding protein 31,269Sus scrofaMutation(s): 0 
Gene Names: RBP3
UniProt
Find proteins for A0A287A908 (Sus scrofa)
Explore A0A287A908 
Go to UniProtKB:  A0A287A908
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A287A908
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Foundation for Polish SciencePolandMAB/2019/12
Foundation for Polish SciencePolandFENG.02.01-IP.05-T005/23
H2020 Marie Curie Actions of the European CommissionEuropean UnionPAN.BFB.S.BDN.315.022.2022

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection