[English] 日本語
Yorodumi
- PDB-5sy1: Structure of the STRA6 receptor for retinol uptake in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5sy1
TitleStructure of the STRA6 receptor for retinol uptake in complex with calmodulin
Components
  • Calmodulin
  • STRA6
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 / retinol transport / retinol transmembrane transporter activity / chordate embryonic development / retinal binding / retinol binding / enzyme regulator activity / signaling receptor activity / molecular adaptor activity / calmodulin binding ...vitamin A import into cell / retinol transport / retinol transmembrane transporter activity / chordate embryonic development / retinal binding / retinol binding / enzyme regulator activity / 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 / : / 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8315
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
1


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

-
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 / 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


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

-
Experimental details

-
Experiment

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

-
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).

-
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 FIELD
Image recordingElectron dose: 100 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more