5HBS

Crystal structure of human cellular retinol binding protein 1 in complex with all-trans-retinol at 0.89 angstrom.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Ligand Binding Induces Conformational Changes in Human Cellular Retinol-binding Protein 1 (CRBP1) Revealed by Atomic Resolution Crystal Structures.

Silvaroli, J.A.Arne, J.M.Chelstowska, S.Kiser, P.D.Banerjee, S.Golczak, M.

(2016) J.Biol.Chem. 291: 8528-8540

  • DOI: 10.1074/jbc.M116.714535
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Important in regulating the uptake, storage, and metabolism of retinoids, cellular retinol-binding protein 1 (CRBP1) is essential for trafficking vitamin A through the cytoplasm. However, the molecular details of ligand uptake and targeted release by ...

    Important in regulating the uptake, storage, and metabolism of retinoids, cellular retinol-binding protein 1 (CRBP1) is essential for trafficking vitamin A through the cytoplasm. However, the molecular details of ligand uptake and targeted release by CRBP1 remain unclear. Here we report the first structure of CRBP1 in a ligand-free form as well as ultra-high resolution structures of this protein bound to either all-trans-retinol or retinylamine, the latter a therapeutic retinoid that prevents light-induced retinal degeneration. Superpositioning of human apo- and holo-CRBP1 revealed major differences within segments surrounding the entrance to the retinoid-binding site. These included α-helix II and hairpin turns between β-strands βC-βD and βE-βF as well as several side chains, such as Phe-57, Tyr-60, and Ile-77, that change their orientations to accommodate the ligand. Additionally, we mapped hydrogen bond networks inside the retinoid-binding cavity and demonstrated their significance for the ligand affinity. Analyses of the crystallographic B-factors indicated several regions with higher backbone mobility in the apoprotein that became more rigid upon retinoid binding. This conformational flexibility of human apo-CRBP1 facilitates interaction with the ligands, whereas the more rigid holoprotein structure protects the labile retinoid moiety during vitamin A transport. These findings suggest a mechanism of induced fit upon ligand binding by mammalian cellular retinol-binding proteins.


    Organizational Affiliation

    From the Department of Pharmacology and.,From the Department of Pharmacology and the Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, mxg149@case.edu.,From the Department of Pharmacology and the Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio 44106.,the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, and the Northeastern Collaborative Access Team, Argonne National Laboratory, Argonne, Illinois 60439.,From the Department of Pharmacology and the Laboratory of Hematology and Flow Cytometry, Department of Hematology, Military Institute of Medicine, Warsaw 04-141, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinol-binding protein 1
A
140Homo sapiensMutation(s): 0 
Gene Names: RBP1 (CRBP1)
Find proteins for P09455 (Homo sapiens)
Go to Gene View: RBP1
Go to UniProtKB:  P09455
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RTL
Query on RTL

Download SDF File 
Download CCD File 
A
RETINOL
C20 H30 O
FPIPGXGPPPQFEQ-OVSJKPMPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RTLKd: 18.5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.217α = 90.00
b = 49.769β = 90.00
c = 73.480γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye InstituteUnited StatesEY023948
Department of Veterans AffairsUnited StatesIK2BX002683

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references
  • Version 1.2: 2016-05-11
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations