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- EMDB-19883: Cryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Giq he... -

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Entry
Database: EMDB / ID: EMD-19883
TitleCryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Giq heterotrimer
Map data
Sample
  • Complex: Ternary complex of Jumping Spider Rhodopsin-1 with a chimeric Giq heterotrimer
    • Complex: Jumping Spider Rhodopsin-1
      • Protein or peptide: Kumopsin1
    • Complex: Human Gi/Jumping Spider Gq Chimera
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Ligand: 11,20-Ethanoretinal
KeywordsOpsin / GPCR / G protein / Signaling Complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


photoreceptor activity / phototransduction / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / adenylate cyclase regulator activity ...photoreceptor activity / phototransduction / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / adenylate cyclase regulator activity / regulation of mitotic spindle organization / cellular response to forskolin / visual perception / Regulation of insulin secretion / G protein-coupled receptor binding / positive regulation of cholesterol biosynthetic process / G protein-coupled receptor activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / response to peptide hormone / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / GDP binding / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / G protein activity / GTPase binding / Ca2+ pathway / retina development in camera-type eye / cell cortex / midbody / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell population proliferation / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / synapse / protein-containing complex binding / nucleolus / GTP binding / magnesium ion binding / signal transduction / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Opsin lateral eye type / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. ...Opsin lateral eye type / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kumopsin1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHasarius adansoni (spider) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.15 Å
AuthorsTejero O / Pamula F / Koyanagi M / Nagata T / Afanasyev P / Das I / Deupi X / Sheves M / Terakita A / Schertler GFX ...Tejero O / Pamula F / Koyanagi M / Nagata T / Afanasyev P / Das I / Deupi X / Sheves M / Terakita A / Schertler GFX / Rodrigues MJ / Tsai C-J
Funding supportEuropean Union, Switzerland, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)951644European Union
H2020 Marie Curie Actions of the European Commission701647European Union
Swiss National Science Foundation192760 Switzerland
Swiss National Science Foundation18563 Switzerland
CitationJournal: Nat Commun / Year: 2024
Title: Active state structures of a bistable visual opsin bound to G proteins.
Authors: Oliver Tejero / Filip Pamula / Mitsumasa Koyanagi / Takashi Nagata / Pavel Afanasyev / Ishita Das / Xavier Deupi / Mordechai Sheves / Akihisa Terakita / Gebhard F X Schertler / Matthew J ...Authors: Oliver Tejero / Filip Pamula / Mitsumasa Koyanagi / Takashi Nagata / Pavel Afanasyev / Ishita Das / Xavier Deupi / Mordechai Sheves / Akihisa Terakita / Gebhard F X Schertler / Matthew J Rodrigues / Ching-Ju Tsai /
Abstract: Opsins are G protein-coupled receptors (GPCRs) that have evolved to detect light stimuli and initiate intracellular signaling cascades. Their role as signal transducers is critical to light ...Opsins are G protein-coupled receptors (GPCRs) that have evolved to detect light stimuli and initiate intracellular signaling cascades. Their role as signal transducers is critical to light perception across the animal kingdom. Opsins covalently bind to the chromophore 11-cis retinal, which isomerizes to the all-trans isomer upon photon absorption, causing conformational changes that result in receptor activation. Monostable opsins, responsible for vision in vertebrates, release the chromophore after activation and must bind another retinal molecule to remain functional. In contrast, bistable opsins, responsible for non-visual light perception in vertebrates and for vision in invertebrates, absorb a second photon in the active state to return the chromophore and protein to the inactive state. Structures of bistable opsins in the activated state have proven elusive, limiting our understanding of how they function as bidirectional photoswitches. Here we present active state structures of a bistable opsin, jumping spider rhodopsin isoform-1 (JSR1), in complex with its downstream signaling partners, the G and G heterotrimers. These structures elucidate key differences in the activation mechanisms between monostable and bistable opsins, offering essential insights for the rational engineering of bistable opsins into diverse optogenetic tools to control G protein signaling pathways.
History
DepositionMar 19, 2024-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19883.png

Downloads & links

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Map

FileDownload / File: emd_19883.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 240 pix.
= 244.8 Å		1.02 Å/pix.
x 240 pix.
= 244.8 Å		1.02 Å/pix.
x 240 pix.
= 244.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.381237 - 2.2483323
Average (Standard dev.)0.004114413 (±0.057748906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 244.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19883_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19883_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of Jumping Spider Rhodopsin-1 with a chimeric Giq...

EntireName: Ternary complex of Jumping Spider Rhodopsin-1 with a chimeric Giq heterotrimer
Components
  • Complex: Ternary complex of Jumping Spider Rhodopsin-1 with a chimeric Giq heterotrimer
    • Complex: Jumping Spider Rhodopsin-1
      • Protein or peptide: Kumopsin1
    • Complex: Human Gi/Jumping Spider Gq Chimera
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Ligand: 11,20-Ethanoretinal

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Supramolecule #1: Ternary complex of Jumping Spider Rhodopsin-1 with a chimeric Giq...

SupramoleculeName: Ternary complex of Jumping Spider Rhodopsin-1 with a chimeric Giq heterotrimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Jumping Spider Rhodopsin-1

SupramoleculeName: Jumping Spider Rhodopsin-1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Hasarius adansoni (spider)

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Supramolecule #3: Human Gi/Jumping Spider Gq Chimera

SupramoleculeName: Human Gi/Jumping Spider Gq Chimera / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: Guanine nucleotide-binding protein G(i) subunit alpha-1 including the following mutations: A31R, D193S, L194I, D337C, T340K, V342T, I344L, K345Q, D350E, G352N, F354V
Source (natural)Organism: Hasarius adansoni (spider)

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Supramolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

SupramoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

SupramoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Kumopsin1

MacromoleculeName: Kumopsin1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hasarius adansoni (spider)
Molecular weightTheoretical: 37.282402 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NISIVDLLPE DMLPMIHEHW YKFPPMETSM HYILGMLIIV IGIISVSGNG VVMYLMMTVK NLRTPGNFLV LNLALSDFGM LFFMMPTMS INCFAETWVI GPFMCELYGM IGSLFGSASI WSLVMITLDR YNVIVKGMAG KPLTKVGALL RMLFVWIWSL G WTIAPMYG ...String:
NISIVDLLPE DMLPMIHEHW YKFPPMETSM HYILGMLIIV IGIISVSGNG VVMYLMMTVK NLRTPGNFLV LNLALSDFGM LFFMMPTMS INCFAETWVI GPFMCELYGM IGSLFGSASI WSLVMITLDR YNVIVKGMAG KPLTKVGALL RMLFVWIWSL G WTIAPMYG WSRYVPEGSM TSCTIDYIDT AINPMSYLIA YAIFVYFVPL FIIIYCYAFI VMQVAAHEKS LREQAKKMNI KS LRSNEDN KKASAEFRLA KVAFMTICCW FMAWTPYLTL SFLGIFSDRT WLTPMTSVWG AIFAKASACY NPIVYGISHP KYR AALHDK F

UniProtKB: Kumopsin1

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Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 2
Details: Human Gi/Jumping Spider Gq Chimera,Human Gi/Jumping Spider Gq Chimera
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.32498 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: CTLSAEDKAA VERSKMIDRN LREDGEKARR EVKLLLLGAG ESGKSTIVKQ MKIIHEAGYS EEECKQYKAV VYSNTIQSII AIIRAMGRL KIDFGDSARA DDARQLFVLA GAAEEGFMTA ELAGVIKRLW KDSGVQACFN RSREYQLNDS AAYYLNDLDR I AQPNYIPT ...String:
CTLSAEDKAA VERSKMIDRN LREDGEKARR EVKLLLLGAG ESGKSTIVKQ MKIIHEAGYS EEECKQYKAV VYSNTIQSII AIIRAMGRL KIDFGDSARA DDARQLFVLA GAAEEGFMTA ELAGVIKRLW KDSGVQACFN RSREYQLNDS AAYYLNDLDR I AQPNYIPT QQDVLRTRVK TTGIVETHFT FKSIHFKMFD VGGQRSERKK WIHCFEGVTA IIFCVALSDY DLVLAEDEEM NR MHESMKL FDSICNNKWF TDTSIILFLN KKDLFEEKIK KSPLTICYPE YAGSNTYEEA AAYIQCQFED LNKRKDTKEI YTH FTCATD TKNVQFVFCA VKDTILQNNL KECNLV

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.285734 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLII WDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR FLDDNQIVTS S GDTTCALW ...String:
SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLII WDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR FLDDNQIVTS S GDTTCALW DIETGQQTTT FTGHTGDVMS LSLAPDTRLF VSGACDASAK LWDVREGMCR QTFTGHESDI NAICFFPNGN AF ATGSDDA TCRLFDLRAD QELMTYSHDN IICGITSVSF SKSGRLLLAG YDDFNCNVWD ALKADRAGVL AGHDNRVSCL GVT DDGMAV ATGSWDSFLK IWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.633625 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
NTASIAQARK LVEQLKMEAN IDRIKVSKAA ADLMAYCEAH AKEDPLLTPV PASENPFREK

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #5: 11,20-Ethanoretinal

MacromoleculeName: 11,20-Ethanoretinal / type: ligand / ID: 5 / Number of copies: 1 / Formula: A1H6M
Molecular weightTheoretical: 310.473 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8.5 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134167
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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