|Entry||Database: EMDB / ID: EMD-23977|
|Title||Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin|
|Map data||Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin|
|Function / homology|
Function and homology information
rhodopsin kinase / rhodopsin kinase activity / The canonical retinoid cycle in rods (twilight vision) / Opsins / VxPx cargo-targeting to cilium / regulation of rhodopsin mediated signaling pathway / rod photoreceptor outer segment / G protein-coupled receptor complex / absorption of visible light / opsin binding ...rhodopsin kinase / rhodopsin kinase activity / The canonical retinoid cycle in rods (twilight vision) / Opsins / VxPx cargo-targeting to cilium / regulation of rhodopsin mediated signaling pathway / rod photoreceptor outer segment / G protein-coupled receptor complex / absorption of visible light / opsin binding / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / 11-cis retinal binding / rhodopsin mediated signaling pathway / cellular response to light stimulus / sperm head plasma membrane / Inactivation, recovery and regulation of the phototransduction cascade / arrestin family protein binding / phototransduction, visible light / Activation of the phototransduction cascade / thermotaxis / detection of temperature stimulus involved in thermoception / outer membrane / photoreceptor cell maintenance / photoreceptor outer segment membrane / G alpha (i) signalling events / G-protein alpha-subunit binding / response to light stimulus / photoreceptor outer segment / phototransduction / regulation of signal transduction / sperm midpiece / visual perception / photoreceptor disc membrane / guanyl-nucleotide exchange factor activity / retina development in camera-type eye / cell-cell junction / G protein-coupled receptor signaling pathway / protein kinase activity / protein autophosphorylation / Golgi membrane / protein phosphorylation / signal transduction / zinc ion binding / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Rhodopsin kinase GRK1 / Rhodopsin kinase, catalytic domain / GPCR kinase / Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Regulator of G protein signaling domain ...Rhodopsin kinase GRK1 / Rhodopsin kinase, catalytic domain / GPCR kinase / Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Rhodopsin / Rhodopsin kinase GRK1
Similarity search - Component
|Biological species||Bos taurus (cattle) / Bovine (cattle)|
|Method||single particle reconstruction / cryo EM / Resolution: 5.8 Å|
|Authors||Chen Q / Li Z / Chang L / Tesmer JJG|
|Funding support|| United States, 4 items |
|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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_23977.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Annotation||Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.08 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire : Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin
|Entire||Name: Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin|
-Supramolecule #1: Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin
|Supramolecule||Name: Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin|
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
|Source (natural)||Organism: Bos taurus (cattle)|
-Macromolecule #1: Rhodopsin kinase GRK1
|Macromolecule||Name: Rhodopsin kinase GRK1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: rhodopsin kinase|
|Source (natural)||Organism: Bos taurus (cattle)|
|Molecular weight||Theoretical: 61.542012 KDa|
|Recombinant expression||Organism: Spodoptera frugiperda (fall armyworm)|
|Sequence||String: MDFGELETVV ANSAFIAARG SFDASSGPAS RDRKYLARLK LPPLSKCEAL RESLDLGFEG MCLEQPIGKR LFQQFLRTHE QHGPALQLW KDIEDYDTAD DALRPQKAQA LRAAYLEPQA QLFCSFLDAE TVARARAGAG DGLFQPLLRA VLAHLGQAPF Q EFLDSLYF ...String: |
MDFGELETVV ANSAFIAARG SFDASSGPAS RDRKYLARLK LPPLSKCEAL RESLDLGFEG MCLEQPIGKR LFQQFLRTHE QHGPALQLW KDIEDYDTAD DALRPQKAQA LRAAYLEPQA QLFCSFLDAE TVARARAGAG DGLFQPLLRA VLAHLGQAPF Q EFLDSLYF LRFLQWKWLE AQPMGEDWFL DFRVLGRGGF GEVFACQMKA TGKLYACKKL NKKRLKKRKG YQGAMVEKKI LA KVHSRFI VSLAYAFETK TDLCLVMTIM NGGDIRYHIY NVDEDNPGFQ EPRAIFYTAQ IVSGLEHLHQ RNIIYRDLKP ENV LLDDDG NVRISDLGLA VELKAGQTKT KGYAGTPGFM APELLLGEEY DFSVDYFALG VTLYEMIAAR GPFRARGEKV ENKE LKQRV LEQAVTYPDK FSPASKDFCE ALLQKDPEKR LGFRDGSCDG LRTHPLFRDI SWRQLEAGML TPPFVPDSRT VYAKN IQDV GAFEEVKGVA FEKADTEFFQ EFASGTCPIP WQEEMIETGV FGDLNVWRPD GVDHHHHHH
-Macromolecule #2: Rhodopsin
|Macromolecule||Name: Rhodopsin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO|
|Source (natural)||Organism: Bovine (cattle)|
|Molecular weight||Theoretical: 39.031457 KDa|
|Sequence||String: MNGTEGPNFY VPFSNKTGVV RSPFEAPQYY LAEPWQFSML AAYMFLLIML GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVFG GFTTTLYTSL HGYFVFGPTG CNLEGFFATL GGEIALWSLV VLAIERYVVV CKPMSNFRFG ENHAIMGVAF T WVMALACA ...String: |
MNGTEGPNFY VPFSNKTGVV RSPFEAPQYY LAEPWQFSML AAYMFLLIML GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVFG GFTTTLYTSL HGYFVFGPTG CNLEGFFATL GGEIALWSLV VLAIERYVVV CKPMSNFRFG ENHAIMGVAF T WVMALACA APPLVGWSRY IPEGMQCSCG IDYYTPHEET NNESFVIYMF VVHFIIPLIV IFFCYGQLVF TVKEAAAQQQ ES ATTQKAE KEVTRMVIIM VIAFLICWLP YAGVAFYIFT HQGSDFGPIF MTIPAFFAKT SAVYNPVIYI MMNKQFRNCM VTT LCCGKN PLGDDEASTT VSKTETSQVA PA
-Macromolecule #3: SANGIVAMYCIN
|Macromolecule||Name: SANGIVAMYCIN / type: ligand / ID: 3 / Number of copies: 1 / Formula: SGV|
|Molecular weight||Theoretical: 309.278 Da|
|Chemical component information|
-Macromolecule #4: RETINAL
|Macromolecule||Name: RETINAL / type: ligand / ID: 4 / Number of copies: 1 / Formula: RET|
|Molecular weight||Theoretical: 284.436 Da|
|Chemical component information|
|Processing||single particle reconstruction|
|Vitrification||Cryogen name: ETHANE|
|Microscope||FEI TITAN KRIOS|
|Electron beam||Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN|
|Electron optics||Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2|
Model: Titan Krios / Image courtesy: FEI Company
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