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Yorodumi- PDB-5sy1: Structure of the STRA6 receptor for retinol uptake in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 5sy1 | ||||||
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Title | Structure of the STRA6 receptor for retinol uptake in complex with calmodulin | ||||||
Components |
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Keywords | MEMBRANE 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 | ||||||
Biological species | Danio rerio (zebrafish) Spodoptera frugiperda (fall armyworm) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Clarke, O.B. / Chen, Y. / Mancia, F. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5sy1.cif.gz | 271.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sy1.ent.gz | 218.3 KB | Display | PDB format |
PDBx/mmJSON format | 5sy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5sy1_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5sy1_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5sy1_validation.xml.gz | 49.4 KB | Display | |
Data in CIF | 5sy1_validation.cif.gz | 75.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/5sy1 ftp://data.pdbj.org/pub/pdb/validation_reports/sy/5sy1 | HTTPS FTP |
-Related structure data
Related structure data | 8315MC 5k8qC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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 | 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 / #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of zebrafish (D. rerio) STRA6 with copurified calmodulin reconstituted in amphipol A8-35 Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pIEX/Bac-1 |
Buffer solution | pH: 7 |
Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 |
Vitrification | Instrument: 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). |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 100 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_2427: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56615 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||||||||||||||
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