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Yorodumi- EMDB-23980: Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23980 | |||||||||||||||
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Title | Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin and Fab6 | |||||||||||||||
Map data | Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin and Fab6 | |||||||||||||||
Sample |
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Function / homology | Function and homology information rhodopsin kinase / rhodopsin kinase activity / Opsins / VxPx cargo-targeting to cilium / opsin binding / regulation of opsin-mediated signaling pathway / 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 / opsin binding / regulation of opsin-mediated signaling pathway / 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 / outer membrane / response to light intensity / 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 / photoreceptor disc membrane / microtubule cytoskeleton organization / 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 | Homo sapiens (human) / Bos taurus (cattle) / Bovine (cattle) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||||||||
Authors | Chen Q / Tesmer JJG | |||||||||||||||
Funding support | United States, 4 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23980.map.gz | 230.3 MB | EMDB map data format | |
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Header (meta data) | emd-23980-v30.xml emd-23980.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23980_fsc.xml | 13.9 KB | Display | FSC data file |
Images | emd_23980.png | 49.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23980 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23980 | HTTPS FTP |
-Validation report
Summary document | emd_23980_validation.pdf.gz | 427.6 KB | Display | EMDB validaton report |
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Full document | emd_23980_full_validation.pdf.gz | 427.2 KB | Display | |
Data in XML | emd_23980_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | emd_23980_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23980 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23980 | HTTPS FTP |
-Related structure data
Related structure data | 7mtbMC 7mt8C 7mt9C 7mtaC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23980.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin and Fab6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin...
Entire | Name: Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin stabilized by Fab6 |
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Components |
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-Supramolecule #1: Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin...
Supramolecule | Name: Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin stabilized by Fab6 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: Fab6 Heavy and Light Chains
Supramolecule | Name: Fab6 Heavy and Light Chains / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Rhodopsin kinase, rhodopsin
Supramolecule | Name: Rhodopsin kinase, rhodopsin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1, #4 |
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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 |
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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: Fab6 heavy chain
Macromolecule | Name: Fab6 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.170939 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NFSSYSIHWV RQAPGKGLEW VAYISSYYGS TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARHEYGWWND RWGLDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NFSSYSIHWV RQAPGKGLEW VAYISSYYGS TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARHEYGWWND RWGLDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDKTHT |
-Macromolecule #3: Fab6 light chain
Macromolecule | Name: Fab6 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.509039 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSWYGPFT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSWYGPFT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC |
-Macromolecule #4: Rhodopsin
Macromolecule | Name: Rhodopsin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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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 #5: SANGIVAMYCIN
Macromolecule | Name: SANGIVAMYCIN / type: ligand / ID: 5 / Number of copies: 1 / Formula: SGV |
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Molecular weight | Theoretical: 309.278 Da |
Chemical component information | ChemComp-SGV: |
-Macromolecule #6: RETINAL
Macromolecule | Name: RETINAL / type: ligand / ID: 6 / Number of copies: 1 / Formula: RET |
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Molecular weight | Theoretical: 284.436 Da |
Chemical component information | ChemComp-RET: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |