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- EMDB-31340: Fzd7 -Gs complex -

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Basic information

Entry
Database: EMDB / ID: EMD-31340
TitleFzd7 -Gs complex
Map data
Sample
  • Complex: human Frizzled 7 in complex with heterotrimeric Gs
    • Protein or peptide: minGas
    • Protein or peptide: Ggamma
    • Protein or peptide: Nb35
    • Protein or peptide: Frizzled-7
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
KeywordsGPCR / Class F / Frizzled / Fzd7 / Frizzled 7 / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of ectodermal cell fate specification / guanyl nucleotide binding / negative regulation of cardiac muscle cell differentiation / somatic stem cell division / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / non-canonical Wnt signaling pathway / Wnt receptor activity / mesenchymal to epithelial transition / positive regulation of epithelial cell proliferation involved in wound healing / Wnt-protein binding ...negative regulation of ectodermal cell fate specification / guanyl nucleotide binding / negative regulation of cardiac muscle cell differentiation / somatic stem cell division / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / non-canonical Wnt signaling pathway / Wnt receptor activity / mesenchymal to epithelial transition / positive regulation of epithelial cell proliferation involved in wound healing / Wnt-protein binding / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / Class B/2 (Secretin family receptors) / regulation of canonical Wnt signaling pathway / Wnt signaling pathway, planar cell polarity pathway / stem cell population maintenance / PKA activation in glucagon signalling / positive regulation of phosphorylation / negative regulation of cell-substrate adhesion / developmental growth / hair follicle placode formation / canonical Wnt signaling pathway / D1 dopamine receptor binding / intracellular transport / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / activation of adenylate cyclase activity / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway / cellular response to retinoic acid / phosphatidylinositol-4,5-bisphosphate binding / regulation of insulin secretion / cellular response to glucagon stimulus / substrate adhesion-dependent cell spreading / adenylate cyclase activator activity / trans-Golgi network membrane / PDZ domain binding / Asymmetric localization of PCP proteins / positive regulation of JNK cascade / negative regulation of inflammatory response to antigenic stimulus / bone development / G protein-coupled receptor activity / platelet aggregation / cognition / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / recycling endosome membrane / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / neuron differentiation / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / 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 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / sensory perception of smell / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / ADP signalling through P2Y purinoceptor 1 / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / adenylate cyclase-activating dopamine receptor signaling pathway / T cell differentiation in thymus / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / positive regulation of cold-induced thermogenesis / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / G protein activity / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events
Similarity search - Function
Frizzled-7, cysteine-rich Wnt-binding 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. ...Frizzled-7, cysteine-rich Wnt-binding 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. / G-protein alpha subunit, group S / 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 / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 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. / 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
Frizzled-7 / 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(s) subunit alpha isoforms short / GNAS complex locus
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsChen B / Xu L
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences2018YFA0507000 China
CitationJournal: Cell Res / Year: 2021
Title: Cryo-EM structure of constitutively active human Frizzled 7 in complex with heterotrimeric G.
Authors: Lu Xu / Bo Chen / Hannes Schihada / Shane C Wright / Ainoleena Turku / Yiran Wu / Gye-Won Han / Maria Kowalski-Jahn / Pawel Kozielewicz / Carl-Fredrik Bowin / Xianjun Zhang / Chao Li / ...Authors: Lu Xu / Bo Chen / Hannes Schihada / Shane C Wright / Ainoleena Turku / Yiran Wu / Gye-Won Han / Maria Kowalski-Jahn / Pawel Kozielewicz / Carl-Fredrik Bowin / Xianjun Zhang / Chao Li / Michel Bouvier / Gunnar Schulte / Fei Xu /
History
DepositionMay 23, 2021-
Header (metadata) releaseAug 4, 2021-
Map releaseAug 4, 2021-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7evw
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31340.png

Downloads & links

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Map

FileDownload / File: emd_31340.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 192 pix.
= 199.68 Å		1.04 Å/pix.
x 192 pix.
= 199.68 Å		1.04 Å/pix.
x 192 pix.
= 199.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.015
Minimum - Maximum-0.08159127 - 0.1314271
Average (Standard dev.)0.0000547981 (±0.003502711)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 199.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z199.680199.680199.680
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0820.1310.000

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Supplemental data

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Sample components

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Entire : human Frizzled 7 in complex with heterotrimeric Gs

EntireName: human Frizzled 7 in complex with heterotrimeric Gs
Components
  • Complex: human Frizzled 7 in complex with heterotrimeric Gs
    • Protein or peptide: minGas
    • Protein or peptide: Ggamma
    • Protein or peptide: Nb35
    • Protein or peptide: Frizzled-7
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Supramolecule #1: human Frizzled 7 in complex with heterotrimeric Gs

SupramoleculeName: human Frizzled 7 in complex with heterotrimeric Gs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: minGas

MacromoleculeName: minGas / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.907684 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: NSKTEDQRNE EKAQREANKK IEKQLQKDKQ VYRATHRLLL LGADNSGKST IVKQMRILHG GSGGSGGTSG IFETKFQVDK VNFHMFDVG GQRDERRKWI QCFNDVTAII FVVDSSDYNR LQEALNLFKS IWNNRWLRTI SVILFLNKQD LLAEKVLAGK S KIEDYFPE ...String:
NSKTEDQRNE EKAQREANKK IEKQLQKDKQ VYRATHRLLL LGADNSGKST IVKQMRILHG GSGGSGGTSG IFETKFQVDK VNFHMFDVG GQRDERRKWI QCFNDVTAII FVVDSSDYNR LQEALNLFKS IWNNRWLRTI SVILFLNKQD LLAEKVLAGK S KIEDYFPE FARYTTPEDA TPEPGEDPRV TRAKYFIRDE FLRISTASGD GRHYCYPHFT CAVDTENARR IFNDCRDIIQ RM HLRQYEL L

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Macromolecule #2: Ggamma

MacromoleculeName: Ggamma / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.366764 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HHHHHHGGGS DSLEFIASKL AGGGSMASNN TASIAQARKL VEQLKMEANI DRIKVSKAAA DLMAYCEAHA KEDPLLTPVP ASENPFREK KFFSAIL

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Macromolecule #3: Nb35

MacromoleculeName: Nb35 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.054232 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAMQVQLQES GGGLVQPGGS LRLSCAASGF TFSNYKMNWV RQAPGKGLEW VSDISQSGAS ISYTGSVKG RFTISRDNAK NTLYLQMNSL KPEDTAVYYC ARCPAPFTRD CFDVTSTTYA YRGQGTQVTV

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Macromolecule #4: Frizzled-7

MacromoleculeName: Frizzled-7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.137562 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AAAAAAAAAA AAAMKTIIAL SYIFCLVFAD YKDDDDKEKG ISVPDHGFCQ PISIPLCTDI AYNQTILPNL LGHTNQEDAG LEVHQFYPL VKVQCSPELR FFLCSMYAPV CTVLDQAIPP CRSLCERARQ GCEALMNKFG FQWPERLRCE NFPVHGAGEI C VGQNTSDG ...String:
AAAAAAAAAA AAAMKTIIAL SYIFCLVFAD YKDDDDKEKG ISVPDHGFCQ PISIPLCTDI AYNQTILPNL LGHTNQEDAG LEVHQFYPL VKVQCSPELR FFLCSMYAPV CTVLDQAIPP CRSLCERARQ GCEALMNKFG FQWPERLRCE NFPVHGAGEI C VGQNTSDG SGGPGGGPTA YPTAPYLPDL PFTALPPGAS DGRGRPAFPF SCPRQLKVPP YLGYRFLGER DCGAPCEPGR AN GLMYFKE EERRFARLWV GVWSVLCCAS TLFTVLTYLV DMRRFSYPER PIIFLSGCYF MVAVAHVAGF LLEDRAVCVE RFS DDGYRT VAQGTKKEGC TILFMVLYFF GMASSIWWVI LSLTWFLAAG MKWGHEAIEA NSQYFHLAAW AVPAVKTITI LAMG QVDGD LLSGVCYVGL SSVDALRGFV LAPLFVYLFI GTSFLLAGFV SLFRIRTIMK HDGTKTEKLE KLMVRIGVFS VLYTV PATI VLACYFYEQA FREHWERTWL LQTCKSYAVP CPPGHFPPMS PDFTVFMIKY LMTMIVGITT GFWIWSGKTL QSWRRF YHR LSHSSKGETA VHHHHHHHHH HGLNDIFEAQ KIEWHE

UniProtKB: Frizzled-7

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Macromolecule #5: 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: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.41693 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 224750
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8yy8:
Fzd7 -Gs complex

PDB-9ew2:
High resolution structure of FZD7 in complex with miniGs protein

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