5K8Q

Crystal Structure of Calcium-loaded Calmodulin in complex with STRA6 CaMBP2-site peptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.739 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the STRA6 receptor for retinol uptake.

Chen, Y.Clarke, O.B.Kim, J.Stowe, S.Kim, Y.K.Assur, Z.Cavalier, M.Godoy-Ruiz, R.von Alpen, D.C.Manzini, C.Blaner, W.S.Frank, J.Quadro, L.Weber, D.J.Shapiro, L.Hendrickson, W.A.Mancia, F.

(2016) Science 353: --

  • DOI: 10.1126/science.aad8266
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Vitamin A homeostasis is critical to normal cellular function. Retinol-binding protein (RBP) is the sole specific carrier in the bloodstream for hydrophobic retinol, the main form in which vitamin A is transported. The integral membrane receptor STRA ...

    Vitamin A homeostasis is critical to normal cellular function. Retinol-binding protein (RBP) is the sole specific carrier in the bloodstream for hydrophobic retinol, the main form in which vitamin A is transported. The integral membrane receptor STRA6 mediates cellular uptake of vitamin A by recognizing RBP-retinol to trigger release and internalization of retinol. We present the structure of zebrafish STRA6 determined to 3.9-angstrom resolution by single-particle cryo-electron microscopy. STRA6 has one intramembrane and nine transmembrane helices in an intricate dimeric assembly. Unexpectedly, calmodulin is bound tightly to STRA6 in a noncanonical arrangement. Residues involved with RBP binding map to an archlike structure that covers a deep lipophilic cleft. This cleft is open to the membrane, suggesting a possible mode for internalization of retinol through direct diffusion into the lipid bilayer.


    Organizational Affiliation

    Department of Medicine, Columbia University, New York, NY 10032, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Pharmacology and Physiology and Department of Integrative Systems Biology, George Washington University, Washington, DC 20037, USA.,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.,The Center for Biomolecular Therapeutics and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Food Science and Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ 08901, USA.,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA. fm123@cumc.columbia.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calmodulin
A
149Homo sapiensMutation(s): 0 
Gene Names: CALM2 (CAM2, CAMB)
Find proteins for P0DP24 (Homo sapiens)
Go to Gene View: CALM2
Go to UniProtKB:  P0DP24
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Zgc:136689
B
29Danio rerioMutation(s): 0 
Gene Names: stra6
Find proteins for F1RAX4 (Danio rerio)
Go to UniProtKB:  F1RAX4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
B
NON-POLYMERH2 N

--

ACE
Query on ACE
B
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.739 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 156.510α = 90.00
b = 37.230β = 94.35
c = 35.730γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHENIXrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU54 GM095315

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-09-07
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations