+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20222 | |||||||||
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Title | Structure of the Rhodopsin-Transducin Complex | |||||||||
Map data | Rhodopsin-Transducin Complex | |||||||||
Sample |
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Function / homology | Function and homology information detection of light stimulus involved in visual perception / negative regulation of cyclic-nucleotide phosphodiesterase activity / Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / Olfactory Signaling Pathway / absorption of visible light / Sensory perception of sweet, bitter, and umami (glutamate) taste ...detection of light stimulus involved in visual perception / negative regulation of cyclic-nucleotide phosphodiesterase activity / Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / Olfactory Signaling Pathway / absorption of visible light / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / 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 / response to light intensity / Activation of the phototransduction cascade / phototransduction, visible light / outer membrane / detection of temperature stimulus involved in thermoception / photoreceptor cell maintenance / arrestin family protein binding / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / photoreceptor outer segment membrane / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / phototransduction / photoreceptor outer segment / acyl binding / G-protein alpha-subunit binding / response to light stimulus / sperm midpiece / visual perception / photoreceptor inner segment / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / photoreceptor disc membrane / microtubule cytoskeleton organization / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / GDP binding / G-protein beta-subunit binding / heterotrimeric G-protein complex / cell-cell junction / signaling receptor complex adaptor activity / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / GTPase activity / GTP binding / protein kinase binding / zinc ion binding / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) / Bovine (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Gao Y / Hu H / Ramachandran S / Erickson JW / Cerione RA / Skiniotis G | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Mol Cell / Year: 2019 Title: Structures of the Rhodopsin-Transducin Complex: Insights into G-Protein Activation. Authors: Yang Gao / Hongli Hu / Sekar Ramachandran / Jon W Erickson / Richard A Cerione / Georgios Skiniotis / Abstract: Rhodopsin (Rho), a prototypical G-protein-coupled receptor (GPCR) in vertebrate vision, activates the G-protein transducin (G) by catalyzing GDP-GTP exchange on its α subunit (Gα). To elucidate the ...Rhodopsin (Rho), a prototypical G-protein-coupled receptor (GPCR) in vertebrate vision, activates the G-protein transducin (G) by catalyzing GDP-GTP exchange on its α subunit (Gα). To elucidate the determinants of G coupling and activation, we obtained cryo-EM structures of a fully functional, light-activated Rho-G complex in the presence and absence of a G-protein-stabilizing nanobody. The structures illustrate how G overcomes its low basal activity by engaging activated Rho in a conformation distinct from other GPCR-G-protein complexes. Moreover, the nanobody-free structures reveal native conformations of G-protein components and capture three distinct conformers showing the Gα helical domain (αHD) contacting the Gβγ subunits. These findings uncover the molecular underpinnings of G-protein activation by visual rhodopsin and shed new light on the role played by Gβγ during receptor-catalyzed nucleotide exchange. | |||||||||
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_20222.map.gz | 49 MB | EMDB map data format | |
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Header (meta data) | emd-20222-v30.xml emd-20222.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
Images | emd_20222.png | 104.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20222 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20222 | HTTPS FTP |
-Validation report
Summary document | emd_20222_validation.pdf.gz | 495.9 KB | Display | EMDB validaton report |
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Full document | emd_20222_full_validation.pdf.gz | 495.5 KB | Display | |
Data in XML | emd_20222_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_20222_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20222 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20222 | HTTPS FTP |
-Related structure data
Related structure data | 6oy9MC 6oyaC C: citing same article (ref.) M: atomic model generated by this map |
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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_20222.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Rhodopsin-Transducin Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 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-Transducin Complex
Entire | Name: Rhodopsin-Transducin Complex |
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Components |
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-Supramolecule #1: Rhodopsin-Transducin Complex
Supramolecule | Name: Rhodopsin-Transducin Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Molecular weight | Theoretical: 141.8 KDa |
-Supramolecule #2: Transducin
Supramolecule | Name: Transducin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Bos taurus (cattle) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: Rhodopsin
Supramolecule | Name: Rhodopsin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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Source (natural) | Organism: Bos taurus (cattle) |
-Macromolecule #1: Gt-alpha/Gi1-alpha chimera
Macromolecule | Name: Gt-alpha/Gi1-alpha chimera / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 41.188895 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAHHHHHHAM GAGASAEEKH SRELEKKLKE DAEKDARTVK LLLLGAGESG KSTIVKQMKI IHQDGYSLEE CLEFIAIIYG NTLQSILAI VRAMTTLNIQ YGDSARQDDA RKLMHMADTI EEGTMPKEMS DIIQRLWKDS GIQACFDRAS EYQLNDSAGY Y LSDLERLV ...String: MAHHHHHHAM GAGASAEEKH SRELEKKLKE DAEKDARTVK LLLLGAGESG KSTIVKQMKI IHQDGYSLEE CLEFIAIIYG NTLQSILAI VRAMTTLNIQ YGDSARQDDA RKLMHMADTI EEGTMPKEMS DIIQRLWKDS GIQACFDRAS EYQLNDSAGY Y LSDLERLV TPGYVPTEQD VLRSRVKTTG IIETQFSFKD LNFRMFDVGG QRSERKKWIH CFEGVTAIIF CVALSDYDMV LV EDDEVNR MHESMHLFNS ICNNKWFTDT SIILFLNKKD LFEEKIKKSP LSICFPDYAG SNTYEEAGNY IKVQFLELNM RRD VKEIYS HMTCATDTQN VKFVFDAVTD IIIKENLKDC GLF |
-Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bovine (cattle) |
Molecular weight | Theoretical: 37.430957 KDa |
Sequence | String: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL LSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL LSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN |
-Macromolecule #3: Guanine nucleotide-binding protein G(T) subunit gamma-T1
Macromolecule | Name: Guanine nucleotide-binding protein G(T) subunit gamma-T1 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bovine (cattle) |
Molecular weight | Theoretical: 9.337784 KDa |
Sequence | String: MPVINIEDPV INIEDLTEKD KLKMEVDQLK KEVTLERMLV SKCCEEFRDY VEERSGEDPL VKGIPEDKNP FKELKGGCVI S |
-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: RETINAL
Macromolecule | Name: RETINAL / type: ligand / ID: 5 / 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: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 12616 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: BACKBONE TRACE |
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Output model | PDB-6oy9: |