[English] 日本語
Yorodumi
- EMDB-19884: Cryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Gi het... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19884
TitleCryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Gi heterotrimer
Map data
Sample
  • Complex: Ternary complex of Jumping Spider Rhodopsin-1 with a human Gi heterotrimer
    • Complex: Jumping Spider Rhodopsin-1
      • Protein or peptide: Kumopsin1
    • Complex: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • 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(T) subunit gamma-T1
      • Protein or peptide: Guanine nucleotide-binding protein G(T) subunit gamma-T1
  • Ligand: RETINAL
KeywordsOpsin / GPCR / G protein / Signaling Complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / 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 ...Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / 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 / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / Extra-nuclear estrogen signaling / G alpha (z) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / photoreceptor activity / phototransduction / T cell migration / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / visual perception / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Regulation of insulin secretion / G protein-coupled receptor binding / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to peptide hormone / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / GDP binding / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / nucleolus / GTP binding / magnesium ion binding / extracellular exosome / nucleoplasm / membrane / plasma membrane / 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(T) subunit gamma-T1 / 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) / Bos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 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 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19884.png

Downloads & links

-
Map

FileDownload / File: emd_19884.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 339.68 Å		0.85 Å/pix.
x 400 pix.
= 339.68 Å		0.85 Å/pix.
x 400 pix.
= 339.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8492 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.09994756 - 0.15631808
Average (Standard dev.)-0.000033297092 (±0.0016987215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 339.68 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_19884_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_19884_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Ternary complex of Jumping Spider Rhodopsin-1 with a human Gi het...

EntireName: Ternary complex of Jumping Spider Rhodopsin-1 with a human Gi heterotrimer
Components
  • Complex: Ternary complex of Jumping Spider Rhodopsin-1 with a human Gi heterotrimer
    • Complex: Jumping Spider Rhodopsin-1
      • Protein or peptide: Kumopsin1
    • Complex: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • 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(T) subunit gamma-T1
      • Protein or peptide: Guanine nucleotide-binding protein G(T) subunit gamma-T1
  • Ligand: RETINAL

+
Supramolecule #1: Ternary complex of Jumping Spider Rhodopsin-1 with a human Gi het...

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

+
Supramolecule #2: Jumping Spider Rhodopsin-1

SupramoleculeName: Jumping Spider Rhodopsin-1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Hasarius adansoni (spider)

+
Supramolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-1

SupramoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

+
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: #2
Source (natural)Organism: Bos taurus (cattle) / Tissue: Retina

+
Supramolecule #5: Guanine nucleotide-binding protein G(T) subunit gamma-T1

SupramoleculeName: Guanine nucleotide-binding protein G(T) subunit gamma-T1
type: complex / ID: 5 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Bos taurus (cattle) / Tissue: Retina

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

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.616211 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GGSMGCTLSA EDKAAVERSK MIDRNLREDG EKAAREVKLL LLGAGESGKS TIVKQMKIIH EAGYSEEECK QYKAVVYSNT IQSIIAIIR AMGRLKIDFG DSARADDARQ LFVLAGAAEE GFMTAELAGV IKRLWKDSGV QACFNRSREY QLNDSAAYYL N DLDRIAQP ...String:
GGSMGCTLSA EDKAAVERSK MIDRNLREDG EKAAREVKLL LLGAGESGKS TIVKQMKIIH EAGYSEEECK QYKAVVYSNT IQSIIAIIR AMGRLKIDFG DSARADDARQ LFVLAGAAEE GFMTAELAGV IKRLWKDSGV QACFNRSREY QLNDSAAYYL N DLDRIAQP NYIPTQQDVL RTRVKTTGIV ETHFTFKDLH FKMFDVGGQR SERKKWIHCF EGVTAIIFCV ALSDYDLVLA ED EEMNRMH ESMKLFDSIC NNKWFTDTSI ILFLNKKDLF EEKIKKSPLT ICYPEYAGSN TYEEAAAYIQ CQFEDLNKRK DTK EIYTHF TCATDTKNVQ FVFDAVTDVI IKNNLKDCGL F

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

+
Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Tissue: Retina
Molecular weightTheoretical: 37.41693 KDa
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI 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

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

+
Macromolecule #3: Guanine nucleotide-binding protein G(T) subunit gamma-T1

MacromoleculeName: Guanine nucleotide-binding protein G(T) subunit gamma-T1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Tissue: Retina
Molecular weightTheoretical: 8.556918 KDa
SequenceString:
MPVINIEDLT EKDKLKMEVD QLKKEVTLER MLVSKCCEEF RDYVEERSGE DPLVKGIPED KNPFKELKGG CVIS

UniProtKB: Guanine nucleotide-binding protein G(T) subunit gamma-T1

+
Macromolecule #4: Kumopsin1

MacromoleculeName: Kumopsin1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hasarius adansoni (spider)
Molecular weightTheoretical: 42.596293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLPHAAKMAA RVAGDHDGRN ISIVDLLPED MLPMIHEHWY KFPPMETSMH YILGMLIIVI GIISVSGNGV VMYLMMTVKN LRTPGNFLV LNLALSDFGM LFFMMPTMSI NCFAETWVIG PFMCELYGMI GSLFGSASIW SLVMITLDRY NVIVKGMAGK P LTKVGALL ...String:
MLPHAAKMAA RVAGDHDGRN ISIVDLLPED MLPMIHEHWY KFPPMETSMH YILGMLIIVI GIISVSGNGV VMYLMMTVKN LRTPGNFLV LNLALSDFGM LFFMMPTMSI NCFAETWVIG PFMCELYGMI GSLFGSASIW SLVMITLDRY NVIVKGMAGK P LTKVGALL RMLFVWIWSL GWTIAPMYGW SRYVPEGSMT SCTIDYIDTA INPMSYLIAY AIFVYFVPLF IIIYCYAFIV MQ VAAHEKS LREQAKKMNI KSLRSNEDNK KASAEFRLAK VAFMTICCWF MAWTPYLTLS FLGIFSDRTW LTPMTSVWGA IFA KASACY NPIVYGISHP KYRAALHDKF PCLKCGSDSP KGDSASTVAE SEKAGEETSQ VAPA

UniProtKB: Kumopsin1

+
Macromolecule #5: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 5 / Number of copies: 1 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.00 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing #1

Image processing ID1
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 399427
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
Image processing #2

Image processing ID2
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 399427
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more