[English] 日本語
Yorodumi
- EMDB-20190: Structure of human Smoothened-Gi complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: EMD-20190
TitleStructure of human Smoothened-Gi complex
Map data
SampleSmoothened-Gi-Fab complex
  • (Smoothened homolog) x 2
  • (Guanine nucleotide-binding protein ...) x 4
  • Fab light chain, Fab heavy chain
  • Fab light chainFragment antigen-binding
  • Fab heavy chainFragment antigen-binding
  • ligand
Function / homology
Function and homology information


Thrombin signalling through proteinase activated receptors (PARs) / Hedgehog 'on' state / Activation of SMO / BBSome-mediated cargo-targeting to cilium / Hedgehog 'off' state / G alpha (s) signalling events / Prostacyclin signalling through prostacyclin receptor / Adrenaline,noradrenaline inhibits insulin secretion / Ca2+ pathway / G alpha (q) signalling events ...Thrombin signalling through proteinase activated receptors (PARs) / Hedgehog 'on' state / Activation of SMO / BBSome-mediated cargo-targeting to cilium / Hedgehog 'off' state / G alpha (s) signalling events / Prostacyclin signalling through prostacyclin receptor / Adrenaline,noradrenaline inhibits insulin secretion / Ca2+ pathway / G alpha (q) signalling events / G alpha (12/13) signalling events / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / G alpha (i) signalling events / G alpha (z) signalling events / Glucagon-type ligand receptors / Regulation of insulin secretion / Thromboxane signalling through TP receptor / Vasopressin regulates renal water homeostasis via Aquaporins / G beta:gamma signalling through PI3Kgamma / ADP signalling through P2Y purinoceptor 12 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Olfactory Signaling Pathway / PLC beta mediated events / Activation of G protein gated Potassium channels / Glucagon signaling in metabolic regulation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Adenylate cyclase inhibitory pathway / G-protein activation / Activation of the phototransduction cascade / G beta:gamma signalling through BTK / Inactivation, recovery and regulation of the phototransduction cascade / G beta:gamma signalling through CDC42 / Class B/2 (Secretin family receptors) / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Extra-nuclear estrogen signaling / Presynaptic function of Kainate receptors / regulation of heart morphogenesis / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / detection of cell density by contact stimulus involved in contact inhibition / negative regulation of hair follicle development / smoothened signaling pathway involved in ventral spinal cord patterning / ventral midline determination / cerebellar cortex morphogenesis / central nervous system neuron differentiation / epithelial-mesenchymal cell signaling / forebrain morphogenesis / pancreas morphogenesis / positive regulation of hh target transcription factor activity / determination of left/right asymmetry in lateral mesoderm / smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation / atrial septum morphogenesis / left/right axis specification / myoblast migration / regulation of stem cell population maintenance / dentate gyrus development / negative regulation of epithelial cell differentiation / renal system development / ciliary tip / dorsal/ventral neural tube patterning / positive regulation of organ growth / regulation of cAMP-mediated signaling / patched binding / somite development / cardiac muscle cell apoptotic process / G protein-coupled serotonin receptor binding / cellular response to cholesterol / G-protein beta/gamma-subunit complex / sensory perception of taste / cellular response to catecholamine stimulus / positive regulation of protein localization to cell cortex / G protein-coupled acetylcholine receptor signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / positive regulation of branching involved in ureteric bud morphogenesis / protein heterotrimerization / thalamus development / type B pancreatic cell development / positive regulation of multicellular organism growth / mammary gland epithelial cell differentiation / rhodopsin mediated signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / cell cortex region / photoreceptor outer segment membrane / positive regulation of smoothened signaling pathway / G-protein beta-subunit binding / commissural neuron axon guidance / smoothened signaling pathway / ciliary membrane / neural crest cell migration / photoreceptor disc membrane / spectrin binding / regulation of mitotic spindle organization / G-protein beta/gamma-subunit complex binding / negative regulation of synaptic transmission / cellular response to forskolin / cell fate specification / heterotrimeric G-protein complex / anterior/posterior pattern specification / Wnt signaling pathway, calcium modulating pathway / hair follicle morphogenesis
Frizzled cysteine-rich domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Smoothened, transmembrane domain / G-protein gamma-like domain superfamily / WD40-repeat-containing domain superfamily / Smoothened, cysteine-rich domain / G-protein beta WD-40 repeat / WD domain, G-beta repeat / G-protein alpha subunit / GGL domain ...Frizzled cysteine-rich domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Smoothened, transmembrane domain / G-protein gamma-like domain superfamily / WD40-repeat-containing domain superfamily / Smoothened, cysteine-rich domain / G-protein beta WD-40 repeat / WD domain, G-beta repeat / G-protein alpha subunit / GGL domain / Fz domain / Frizzled/Smoothened family membrane region / Trp-Asp (WD) repeats signature. / Smoothened / Frizzled domain / G-protein, gamma subunit / Frizzled/Smoothened, transmembrane domain / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit, group I / G-protein, beta subunit / WD40 repeat / G protein alpha subunit, helical insertion / WD40 repeat, conserved site / Frizzled/secreted frizzled-related protein / G-protein gamma-like domain / WD40/YVTN repeat-like-containing domain superfamily / Guanine nucleotide-binding protein, beta subunit / GPCR, family 2-like / WD40-repeat-containing domain / Frizzled (fz) domain profile. / G-protein gamma subunit domain profile. / Trp-Asp (WD) repeats profile. / G-protein coupled receptors family 2 profile 2. / Trp-Asp (WD) repeats circular profile. / G-alpha domain profile.
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 / Smoothened homolog
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / Resolution: 3.84 Å
AuthorsQi X / Li X
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structure of oxysterol-bound human Smoothened coupled to a heterotrimeric G.
Authors: Xiaofeng Qi / Heng Liu / Bonne Thompson / Jeffrey McDonald / Cheng Zhang / Xiaochun Li /
Abstract: The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F), transduces the Hedgehog signal from the tumour suppressor Patched-1 (PTCH1) to the ...The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F), transduces the Hedgehog signal from the tumour suppressor Patched-1 (PTCH1) to the glioma-associated-oncogene (GLI) transcription factors, which activates the Hedgehog signalling pathway. It has remained unknown how PTCH1 modulates SMO, how SMO is stimulated to form a complex with heterotrimeric G proteins and whether G-protein coupling contributes to the activation of GLI proteins. Here we show that 24,25-epoxycholesterol, which we identify as an endogenous ligand of PTCH1, can stimulate Hedgehog signalling in cells and can trigger G-protein signalling via human SMO in vitro. We present a cryo-electron microscopy structure of human SMO bound to 24(S),25-epoxycholesterol and coupled to a heterotrimeric G protein. The structure reveals a ligand-binding site for 24(S),25-epoxycholesterol in the 7-transmembrane region, as well as a G-coupled activation mechanism of human SMO. Notably, the G protein presents a different arrangement from that of class-A GPCR-G complexes. Our work provides molecular insights into Hedgehog signal transduction and the activation of a class-F GPCR.
Validation ReportPDB-ID: 6ot0

SummaryFull reportAbout validation report
DateDeposition: May 2, 2019 / Header (metadata) release: Jun 12, 2019 / Map release: Jun 12, 2019 / Update: Jun 19, 2019

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6ot0
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_20190.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å
1.07 Å/pix.
x 280 pix.
= 299.6 Å
1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.33 / Movie #1: 0.4
Minimum - Maximum-0.8802892 - 1.5884628
Average (Standard dev.)0.002593234 (±0.067070134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z299.600299.600299.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.8801.5880.003

-
Supplemental data

-
Sample components

+
Entire Smoothened-Gi-Fab complex

EntireName: Smoothened-Gi-Fab complex / Number of components: 11

+
Component #1: protein, Smoothened-Gi-Fab complex

ProteinName: Smoothened-Gi-Fab complex / Recombinant expression: No
MassExperimental: 250 kDa

+
Component #2: protein, Smoothened homolog

ProteinName: Smoothened homolog / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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

ProteinName: Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

+
Component #4: protein, Fab light chain, Fab heavy chain

ProteinName: Fab light chain, Fab heavy chain / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #5: protein, Smoothened homolog

ProteinName: Smoothened homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 62.109387 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #6: protein, Guanine nucleotide-binding protein G(i) subunit alpha-1

ProteinName: Guanine nucleotide-binding protein G(i) subunit alpha-1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.414047 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

+
Component #7: protein, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subuni...

ProteinName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.744371 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

+
Component #8: protein, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subuni...

ProteinName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.861143 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

+
Component #9: protein, Fab light chain

ProteinName: Fab light chainFragment antigen-binding / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.258783 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #10: protein, Fab heavy chain

ProteinName: Fab heavy chainFragment antigen-binding / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.788822 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #11: ligand, 17-[3-(3,3-DIMETHYL-OXIRANYL)-1-METHYL-PROPYL]-10,13-DIME...

LigandName: 17-[3-(3,3-DIMETHYL-OXIRANYL)-1-METHYL-PROPYL]-10,13-DIMETHYL-2,3,4,7,8,9,10,11,12,13,14,15,16,17-TETRADECAHYDRO-1H-CYCLOPENTA[A]PHENANTHREN-3-OL
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.400637 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle
Sample solutionpH: 7.5
VitrificationCryogen name: NONE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: DARK FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 141100
3D reconstructionResolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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