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Yorodumi- PDB-7mt8: Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mt8 | |||||||||||||||
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Title | Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Signaling protein / GPCR / signal desensitization / Kinase | |||||||||||||||
Function / homology | Function and homology information rhodopsin kinase / rhodopsin kinase activity / Opsins / VxPx cargo-targeting to cilium / regulation of opsin-mediated signaling pathway / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / absorption of visible light / The canonical retinoid cycle in rods (twilight vision) ...rhodopsin kinase / rhodopsin kinase activity / Opsins / VxPx cargo-targeting to cilium / regulation of opsin-mediated signaling pathway / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / absorption of visible light / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly / 11-cis retinal binding / G protein-coupled photoreceptor activity / rod photoreceptor outer segment / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / Activation of the phototransduction cascade / phototransduction, visible light / response to light intensity / outer membrane / detection of temperature stimulus involved in thermoception / arrestin family protein binding / photoreceptor cell maintenance / photoreceptor outer segment membrane / G alpha (i) signalling events / phototransduction / response to light stimulus / photoreceptor outer segment / G-protein alpha-subunit binding / regulation of signal transduction / sperm midpiece / visual perception / guanyl-nucleotide exchange factor activity / microtubule cytoskeleton organization / photoreceptor disc membrane / cell-cell junction / gene expression / protein autophosphorylation / G protein-coupled receptor signaling pathway / Golgi membrane / signal transduction / zinc ion binding / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Bos taurus (cattle) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||||||||
Authors | Chen, Q. / Chen, C.-L. / Tesmer, J.J.G. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nature / Year: 2021 Title: Structures of rhodopsin in complex with G-protein-coupled receptor kinase 1. Authors: Qiuyan Chen / Manolo Plasencia / Zhuang Li / Somnath Mukherjee / Dhabaleswar Patra / Chun-Liang Chen / Thomas Klose / Xin-Qiu Yao / Anthony A Kossiakoff / Leifu Chang / Philip C Andrews / John J G Tesmer / Abstract: G-protein-coupled receptor (GPCR) kinases (GRKs) selectively phosphorylate activated GPCRs, thereby priming them for desensitization. Although it is unclear how GRKs recognize these receptors, a ...G-protein-coupled receptor (GPCR) kinases (GRKs) selectively phosphorylate activated GPCRs, thereby priming them for desensitization. Although it is unclear how GRKs recognize these receptors, a conserved region at the GRK N terminus is essential for this process. Here we report a series of cryo-electron microscopy single-particle reconstructions of light-activated rhodopsin (Rho*) bound to rhodopsin kinase (GRK1), wherein the N terminus of GRK1 forms a helix that docks into the open cytoplasmic cleft of Rho*. The helix also packs against the GRK1 kinase domain and stabilizes it in an active configuration. The complex is further stabilized by electrostatic interactions between basic residues that are conserved in most GPCRs and acidic residues that are conserved in GRKs. We did not observe any density for the regulator of G-protein signalling homology domain of GRK1 or the C terminus of rhodopsin. Crosslinking with mass spectrometry analysis confirmed these results and revealed dynamic behaviour in receptor-bound GRK1 that would allow the phosphorylation of multiple sites in the receptor tail. We have identified GRK1 residues whose mutation augments kinase activity and crosslinking with Rho*, as well as residues that are involved in activation by acidic phospholipids. From these data, we present a general model for how a small family of protein kinases can recognize and be activated by hundreds of different GPCRs. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7mt8.cif.gz | 654.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mt8.ent.gz | 555 KB | Display | PDB format |
PDBx/mmJSON format | 7mt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mt8_validation.pdf.gz | 880.6 KB | Display | wwPDB validaton report |
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Full document | 7mt8_full_validation.pdf.gz | 897.8 KB | Display | |
Data in XML | 7mt8_validation.xml.gz | 83.5 KB | Display | |
Data in CIF | 7mt8_validation.cif.gz | 127 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/7mt8 ftp://data.pdbj.org/pub/pdb/validation_reports/mt/7mt8 | HTTPS FTP |
-Related structure data
Related structure data | 23977MC 7mt9C 7mtaC 7mtbC 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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1 |
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Number of models | 6 |
-Components
#1: Protein | Mass: 61542.012 Da / Num. of mol.: 1 / Mutation: S5E, S488E, T489E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK1, RHOK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28327, rhodopsin kinase |
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#2: Protein | Mass: 39031.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02699 |
#3: Chemical | ChemComp-SGV / |
#4: Chemical | ChemComp-RET / |
Has ligand of interest | N |
-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: Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Bos taurus (cattle) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132721 / Symmetry type: POINT |