[English] 日本語
Yorodumi
- EMDB-27062: Cryo-EM structure of the unliganded mSMO-PGS2 in a lipidic environment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27062
TitleCryo-EM structure of the unliganded mSMO-PGS2 in a lipidic environment
Map data
Sample
  • Complex: mSMO-PGS2
    • Protein or peptide: Smoothened homolog, GlgA glycogen synthase chimera
  • Ligand: CHOLESTEROL
KeywordsG-protein coupled receptor / Smoothened / unliganded state / lipid system / MEMBRANE PROTEIN
Function / homology
Function and homology information


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 / negative regulation of hair follicle development / negative regulation of hepatocyte proliferation / 9+0 non-motile cilium / 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 / negative regulation of hair follicle development / negative regulation of hepatocyte proliferation / 9+0 non-motile cilium / central nervous system neuron differentiation / regulation of somatic stem cell population maintenance / pancreas morphogenesis / mesenchymal to epithelial transition / epithelial-mesenchymal cell signaling / : / myoblast migration / atrial septum morphogenesis / contact inhibition / 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 / patched binding / thalamus development / somite development / positive regulation of branching involved in ureteric bud morphogenesis / type B pancreatic cell development / dorsal/ventral neural tube patterning / forebrain morphogenesis / cellular response to cholesterol / 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 neural precursor cell proliferation / commissural neuron axon guidance / positive regulation of multicellular organism growth / dopaminergic neuron differentiation / oxysterol binding / digestive tract development / positive regulation of smoothened signaling pathway / positive regulation of vascular associated smooth muscle cell migration / dorsal/ventral pattern formation / determination of left/right symmetry / cell fate specification / neural crest cell migration / cAMP-dependent protein kinase inhibitor activity / ciliary membrane / positive regulation of mesenchymal cell proliferation / anterior/posterior pattern specification / 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 / protein localization to nucleus / neuroblast proliferation / hair follicle development / developmental growth / endoplasmic reticulum-Golgi intermediate compartment / embryonic organ development / vasculogenesis / skeletal muscle fiber development / positive regulation of autophagy / axonal growth cone / heart morphogenesis / homeostasis of number of cells within a tissue / epithelial cell differentiation / centriole / ossification / protein sequestering activity / negative regulation of protein phosphorylation / epithelial cell proliferation / central nervous system development / positive regulation of epithelial cell proliferation / caveola / astrocyte activation / G protein-coupled receptor activity / multicellular organism growth / cilium / cerebral cortex development / osteoblast differentiation / positive regulation of protein import into nucleus / protein import into nucleus / endocytic vesicle membrane / late endosome / gene expression / regulation of gene expression
Similarity search - Function
Smoothened, transmembrane domain / Smoothened, cysteine-rich domain / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein ...Smoothened, transmembrane domain / Smoothened, cysteine-rich domain / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2.
Similarity search - Domain/homology
Protein smoothened / Glycogen synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhang K / Wu H / Hoppe N / Manglik A / Cheng Y
Funding support France, United States, 3 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)LT000471/2017-L France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140847 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)TR003384 United States
CitationJournal: Nat Commun / Year: 2022
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
DepositionMay 22, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27062.png

Downloads & links

-
Map

FileDownload / File: emd_27062.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.835 Å
Density
Contour LevelBy AUTHOR: 0.0063
Minimum - Maximum-0.037992913 - 0.05168554
Average (Standard dev.)0.000017372107 (±0.0015011403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 213.76 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_27062_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_27062_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : mSMO-PGS2

EntireName: mSMO-PGS2
Components
  • Complex: mSMO-PGS2
    • Protein or peptide: Smoothened homolog, GlgA glycogen synthase chimera
  • Ligand: CHOLESTEROL

-
Supramolecule #1: mSMO-PGS2

SupramoleculeName: mSMO-PGS2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Smoothened homolog, GlgA glycogen synthase chimera

MacromoleculeName: Smoothened homolog, GlgA glycogen synthase chimera / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 80.86818 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Sugar embeddingMaterial: nanodisc
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 68.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6o3c

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90476
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