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- PDB-5sy1: Structure of the STRA6 receptor for retinol uptake in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5sy1
TitleStructure of the STRA6 receptor for retinol uptake in complex with calmodulin
Components
  • Calmodulin
  • STRA6Vitamin A receptor
KeywordsMEMBRANE PROTEIN/CALCIUM BINDING PROTEIN / Vitamin A / retinol / STRA6 / membrane / MEMBRANE PROTEIN-CALCIUM BINDING PROTEIN complex
Function / homology
Function and homology information


vitamin A import into cell / The canonical retinoid cycle in rods (twilight vision) / retinol transport / retinol transmembrane transporter activity / chordate embryonic development / retinal binding / retinol binding / plasma membrane => GO:0005886 / calcium-mediated signaling / signaling receptor activity ...vitamin A import into cell / The canonical retinoid cycle in rods (twilight vision) / retinol transport / retinol transmembrane transporter activity / chordate embryonic development / retinal binding / retinol binding / plasma membrane => GO:0005886 / calcium-mediated signaling / signaling receptor activity / molecular adaptor activity / calmodulin binding / calcium ion binding / identical protein binding / plasma membrane
Similarity search - Function
Receptor for retinol uptake STRA6 / Retinol binding protein receptor / Calmodulin / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
CHOLESTEROL / Calmodulin / Receptor for retinol uptake stra6 / Receptor for retinol uptake stra6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Spodoptera frugiperda (fall armyworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsClarke, O.B. / Chen, Y. / Mancia, F.
CitationJournal: Science / Year: 2016
Title: Structure of the STRA6 receptor for retinol uptake.
Authors: Yunting Chen / Oliver B Clarke / Jonathan Kim / Sean Stowe / Youn-Kyung Kim / Zahra Assur / Michael Cavalier / Raquel Godoy-Ruiz / Desiree C von Alpen / Chiara Manzini / William S Blaner / ...Authors: Yunting Chen / Oliver B Clarke / Jonathan Kim / Sean Stowe / Youn-Kyung Kim / Zahra Assur / Michael Cavalier / Raquel Godoy-Ruiz / Desiree C von Alpen / Chiara Manzini / William S Blaner / Joachim Frank / Loredana Quadro / David J Weber / Lawrence Shapiro / Wayne A Hendrickson / Filippo Mancia /
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 ...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.
History
DepositionAug 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Jul 26, 2017Group: Data collection / Database references / Category: citation / em_image_scans / em_software
Item: _citation.journal_id_CSD / _em_software.details / _em_software.name
Revision 1.3Jul 18, 2018Group: Data collection / Experimental preparation / Category: em_sample_support / em_software / Item: _em_sample_support.grid_type / _em_software.name
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
C: Calmodulin
A: STRA6
B: STRA6
D: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,84814
Polymers184,7544
Non-polymers1,09410
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area25860 Å2
ΔGint-213 kcal/mol
Surface area73610 Å2

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Components

#1: Protein Calmodulin /


Mass: 16825.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A1C7D1B9*PLUS
#2: Protein STRA6 / Vitamin A receptor / Zgc:136689


Mass: 75551.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: stra6, zgc:136689 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A4IGB6, UniProt: F1RAX4*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of zebrafish (D. rerio) STRA6 with copurified calmodulin reconstituted in amphipol A8-35
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Danio rerio (zebrafish)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pIEX/Bac-1
Buffer solutionpH: 7
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K
Details: 3 uL sample applied, 3-4 second blot time, 30 second wait time, blot force 3, grid blotted from both sides, plunged into liquid ethane (FEI VITROBOT MARK IV).

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 100 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2427: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELION1.3particle selection
2Leginonimage acquisition
4CTFFIND44.0.17CTF correction
7Coot0.8.4model fitting
10RELION1.3final Euler assignment
12RELION1.33D reconstruction
13PHENIXdev-2481model refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56615 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01311760
ELECTRON MICROSCOPYf_angle_d1.24215914
ELECTRON MICROSCOPYf_dihedral_angle_d6.2976938
ELECTRON MICROSCOPYf_chiral_restr0.111872
ELECTRON MICROSCOPYf_plane_restr0.0081978

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