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- EMDB-27062: Cryo-EM structure of the unliganded mSMO-PGS2 in a lipidic environment -
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Open data
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Basic information
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Title | Cryo-EM structure of the unliganded mSMO-PGS2 in a lipidic environment | ||||||||||||
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![]() | G-protein coupled receptor / Smoothened / unliganded state / lipid system / MEMBRANE PROTEIN | ||||||||||||
Function / homology | ![]() BBSome-mediated cargo-targeting to cilium / regulation of localization / ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / Activation of SMO / regulation of heart morphogenesis / contact inhibition / negative regulation of hair follicle development / negative regulation of hepatocyte proliferation / central nervous system neuron differentiation ...BBSome-mediated cargo-targeting to cilium / regulation of localization / ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / Activation of SMO / regulation of heart morphogenesis / contact inhibition / negative regulation of hair follicle development / negative regulation of hepatocyte proliferation / central nervous system neuron differentiation / 9+0 non-motile cilium / pancreas morphogenesis / regulation of somatic stem cell population maintenance / mesenchymal to epithelial transition / epithelial-mesenchymal cell signaling / myoblast migration / atrial septum morphogenesis / determination of left/right asymmetry in lateral mesoderm / Hedgehog 'on' state / spinal cord dorsal/ventral patterning / axon extension involved in axon guidance / positive regulation of hepatic stellate cell activation / cell development / glycogen (starch) synthase activity / left/right axis specification / Hedgehog 'off' state / thalamus development / somite development / patched binding / forebrain morphogenesis / cellular response to cholesterol / type B pancreatic cell development / dorsal/ventral neural tube patterning / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of organ growth / smooth muscle tissue development / pattern specification process / cerebellar cortex morphogenesis / mammary gland epithelial cell differentiation / dentate gyrus development / positive regulation of multicellular organism growth / dopaminergic neuron differentiation / commissural neuron axon guidance / oxysterol binding / positive regulation of neural precursor cell proliferation / positive regulation of smoothened signaling pathway / digestive tract development / dorsal/ventral pattern formation / positive regulation of vascular associated smooth muscle cell migration / glycogen biosynthetic process / determination of left/right symmetry / cell fate specification / neural crest cell migration / cAMP-dependent protein kinase inhibitor activity / ciliary membrane / anterior/posterior pattern specification / positive regulation of mesenchymal cell proliferation / negative regulation of epithelial cell differentiation / midgut development / smoothened signaling pathway / hair follicle morphogenesis / positive regulation of neuroblast proliferation / heart looping / negative regulation of DNA binding / odontogenesis of dentin-containing tooth / dendritic growth cone / protein kinase A catalytic subunit binding / endoplasmic reticulum-Golgi intermediate compartment / protein localization to nucleus / hair follicle development / developmental growth / neuroblast proliferation / vasculogenesis / embryonic organ development / positive regulation of autophagy / skeletal muscle fiber development / axonal growth cone / heart morphogenesis / homeostasis of number of cells within a tissue / epithelial cell differentiation / protein sequestering activity / centriole / ossification / negative regulation of protein phosphorylation / epithelial cell proliferation / caveola / central nervous system development / positive regulation of epithelial cell proliferation / G protein-coupled receptor activity / astrocyte activation / multicellular organism growth / cerebral cortex development / cilium / positive regulation of protein import into nucleus / osteoblast differentiation / protein import into nucleus / endocytic vesicle membrane / late endosome / gene expression / regulation of gene expression Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
![]() | Zhang K / Wu H / Hoppe N / Manglik A / Cheng Y | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Fusion protein strategies for cryo-EM study of G protein-coupled receptors. Authors: Kaihua Zhang / Hao Wu / Nicholas Hoppe / Aashish Manglik / Yifan Cheng / ![]() Abstract: Single particle cryogenic-electron microscopy (cryo-EM) is used extensively to determine structures of activated G protein-coupled receptors (GPCRs) in complex with G proteins or arrestins. However, ...Single particle cryogenic-electron microscopy (cryo-EM) is used extensively to determine structures of activated G protein-coupled receptors (GPCRs) in complex with G proteins or arrestins. However, applying it to GPCRs without signaling proteins remains challenging because most receptors lack structural features in their soluble domains to facilitate image alignment. In GPCR crystallography, inserting a fusion protein between transmembrane helices 5 and 6 is a highly successful strategy for crystallization. Although a similar strategy has the potential to broadly facilitate cryo-EM structure determination of GPCRs alone without signaling protein, the critical determinants that make this approach successful are not yet clear. Here, we address this shortcoming by exploring different fusion protein designs, which lead to structures of antagonist bound A adenosine receptor at 3.4 Å resolution and unliganded Smoothened at 3.7 Å resolution. The fusion strategies explored here are likely applicable to cryo-EM interrogation of other GPCRs and small integral membrane proteins. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.9 KB 14.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.2 KB | Display | ![]() |
Images | ![]() | 57.5 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() | 49.6 MB 49.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 825.2 KB | Display | ![]() |
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Full document | ![]() | 824.7 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cxoMC ![]() 7t32C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_27062_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27062_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : mSMO-PGS2
Entire | Name: mSMO-PGS2 |
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Components |
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-Supramolecule #1: mSMO-PGS2
Supramolecule | Name: mSMO-PGS2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Smoothened homolog, GlgA glycogen synthase chimera
Macromolecule | Name: Smoothened homolog, GlgA glycogen synthase chimera / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 80.86818 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: WSHPQFEKEN LYFQSPRLLS HCGRAAHCEP LRYNVCLGSA LPYGATTTLL AGDSDSQEEA HGKLVLWSGL RNAPRCWAVI QPLLCAVYM PKCENDRVEL PSRTLCQATR GPCAIVERER GWPDFLRCTP DHFPEGCPNE VQNIKFNSSG QCEAPLVRTD N PKSWYEDV ...String: WSHPQFEKEN LYFQSPRLLS HCGRAAHCEP LRYNVCLGSA LPYGATTTLL AGDSDSQEEA HGKLVLWSGL RNAPRCWAVI QPLLCAVYM PKCENDRVEL PSRTLCQATR GPCAIVERER GWPDFLRCTP DHFPEGCPNE VQNIKFNSSG QCEAPLVRTD N PKSWYEDV EGCGIQCQNP LFTEAEHQDM HSYIAAFGAV TGLCTLFTLA TFVADWRNSN RYPAVILFYV NACFFVGSIG WL AQFMDGA RREIVCRADG TMRFGEPTSS ETLSCVIIFV IVYYALMAGV VWFVVLTYAW HTSFKALGTT YQPLSGKTSY FHL LTWSLP FVLTVAILAV AQVDGDSVSG ICFVGYKNYR YRAGFVLAPI GLVLIVGGYF LIRGVMTLFS IKSNHPGLLG IDCS FWNES YLTGSRDERK KSLLSKFGMD EGVTFMFIGR FDRGQKGVDV LLKAIEILSS KKEFQEMRFI IIGKGDPELE GWARS LEEK HGNVKVITEM LSREFVRELY GSVDFVIIPS YFEPFGLVAL EAMCLGAIPI ASAVGGLRDI ITNETGILVK AGDPGE LAN AILKALELSR SDLSKFRENC KKRAMSFSDQ ARMDIRLAKN ETMLRLGIFG FLAFGFVLIT FSCHFYDFFN QAEWERS FR DYVLCQANVT IGLPTKKPIP DCEIKNRPSL LVEKINLFAM FGTGIAMSTW VWTKATLLIW RRTWCRLTGH SDDEPKR UniProtKB: Protein smoothened, Glycogen synthase, Protein smoothened |
-Macromolecule #2: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 1 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ![]() ChemComp-CLR: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Sugar embedding | Material: nanodisc |
Vitrification | Cryogen name: ETHANE |
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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: 68.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |