5SY1

Structure of the STRA6 receptor for retinol uptake in complex with calmodulin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1126/science.aad8266
  • Primary Citation of Related Structures:  
    5K8Q, 5SY1

  • 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 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 Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CalmodulinA [auth C],
D
149Spodoptera frugiperdaMutation(s): 0 
UniProt
Find proteins for A0A1C7D1B9 (Spodoptera frugiperda)
Explore A0A1C7D1B9 
Go to UniProtKB:  A0A1C7D1B9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C7D1B9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
STRA6B [auth A],
C [auth B]
670Danio rerioMutation(s): 0 
Gene Names: stra6zgc:136689
Membrane Entity: Yes 
UniProt
Find proteins for F1RAX4 (Danio rerio)
Explore F1RAX4 
Go to UniProtKB:  F1RAX4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1RAX4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
I [auth A],
J [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth C]
F [auth C]
G [auth C]
H [auth C]
K [auth D]
E [auth C],
F [auth C],
G [auth C],
H [auth C],
K [auth D],
L [auth D],
M [auth D],
N [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.3
MODEL REFINEMENTPHENIXdev-2481

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Data collection, Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references