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- EMDB-31360: Cryo-EM structure of human GPR158 in complex with RGS7-Gbeta5 in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-31360
TitleCryo-EM structure of human GPR158 in complex with RGS7-Gbeta5 in a 2:1:1 ratio
Map dataOverall refined map
Sample
  • Complex: GPR158-RGS7-Gb5 in a 2:1:1 ratio
    • Protein or peptide: Probable G-protein coupled receptor 158
    • Protein or peptide: Regulator of G-protein signaling 7
    • Protein or peptide: Guanine nucleotide-binding protein subunit beta-5
KeywordsGPCR / SIGNALING PROTEIN
Function / homology
Function and homology information


G protein-coupled glycine receptor activity / GTPase activator complex / dark adaptation / light adaption / G-protein gamma-subunit binding / negative regulation of voltage-gated calcium channel activity / cell tip / positive regulation of potassium ion transmembrane transport / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion ...G protein-coupled glycine receptor activity / GTPase activator complex / dark adaptation / light adaption / G-protein gamma-subunit binding / negative regulation of voltage-gated calcium channel activity / cell tip / positive regulation of potassium ion transmembrane transport / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion / G protein-coupled dopamine receptor signaling pathway / negative regulation of G protein-coupled receptor signaling pathway / regulation of synapse organization / parallel fiber to Purkinje cell synapse / G-protein alpha-subunit binding / positive regulation of GTPase activity / response to amphetamine / GTPase activator activity / enzyme activator activity / protein localization to plasma membrane / cell projection / postsynaptic density membrane / brain development / cognition / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / transmembrane signaling receptor activity / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / nuclear envelope / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / protein-folding chaperone binding / presynaptic membrane / Ca2+ pathway / 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 / G alpha (q) signalling events / response to ethanol / postsynaptic membrane / Extra-nuclear estrogen signaling / neuron projection / intracellular signal transduction / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / signal transduction / protein-containing complex / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Regulator of G-protein signalling, DHEX domain / G-protein coupled receptor 158/179 / : / : / : / Regulator of G-protein signalling DHEX domain / GPR158/179 extracellular domain / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin ...Regulator of G-protein signalling, DHEX domain / G-protein coupled receptor 158/179 / : / : / : / Regulator of G-protein signalling DHEX domain / GPR158/179 extracellular domain / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / 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 beta WD-40 repeat / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Guanine nucleotide-binding protein subunit beta-5 / Regulator of G-protein signaling 7 / Metabotropic glycine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKim Y / Jeong E
Funding support3 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C301335711
National Research Foundation (NRF, Korea)2017M3A9F6029736
Other privateSSTF-BA1602-14
CitationJournal: Nat Commun / Year: 2021
Title: Structure of the class C orphan GPCR GPR158 in complex with RGS7-Gβ5.
Authors: Eunyoung Jeong / Yoojoong Kim / Jihong Jeong / Yunje Cho /
Abstract: GPR158, a class C orphan GPCR, functions in cognition, stress-induced mood control, and synaptic development. Among class C GPCRs, GPR158 is unique as it lacks a Venus flytrap-fold ligand-binding ...GPR158, a class C orphan GPCR, functions in cognition, stress-induced mood control, and synaptic development. Among class C GPCRs, GPR158 is unique as it lacks a Venus flytrap-fold ligand-binding domain and terminates Gαi/o protein signaling through the RGS7-Gβ5 heterodimer. Here, we report the cryo-EM structures of GPR158 alone and in complex with one or two RGS7-Gβ5 heterodimers. GPR158 dimerizes through Per-Arnt-Sim-fold extracellular and transmembrane (TM) domains connected by an epidermal growth factor-like linker. The TM domain (TMD) reflects both inactive and active states of other class C GPCRs: a compact intracellular TMD, conformations of the two intracellular loops (ICLs) and the TMD interface formed by TM4/5. The ICL2, ICL3, TM3, and first helix of the cytoplasmic coiled-coil provide a platform for the DHEX domain of one RGS7 and the second helix recruits another RGS7. The unique features of the RGS7-binding site underlie the selectivity of GPR158 for RGS7.
History
DepositionMay 25, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.371
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.371
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ewp
  • Surface level: 0.371
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31360.png

Downloads & links

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Map

FileDownload / File: emd_31360.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall refined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 350 pix.
= 374.482 Å		1.07 Å/pix.
x 350 pix.
= 374.482 Å		1.07 Å/pix.
x 350 pix.
= 374.482 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06995 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.371 / Movie #1: 0.371
Minimum - Maximum-1.3871425 - 2.0562553
Average (Standard dev.)-0.001032287 (±0.038186632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 374.48248 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06994857142861.06994857142861.0699485714286
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z374.482374.482374.482
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-1.3872.056-0.001

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Supplemental data

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Additional map: Locally refined map

Fileemd_31360_additional_1.map
AnnotationLocally refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GPR158-RGS7-Gb5 in a 2:1:1 ratio

EntireName: GPR158-RGS7-Gb5 in a 2:1:1 ratio
Components
  • Complex: GPR158-RGS7-Gb5 in a 2:1:1 ratio
    • Protein or peptide: Probable G-protein coupled receptor 158
    • Protein or peptide: Regulator of G-protein signaling 7
    • Protein or peptide: Guanine nucleotide-binding protein subunit beta-5

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Supramolecule #1: GPR158-RGS7-Gb5 in a 2:1:1 ratio

SupramoleculeName: GPR158-RGS7-Gb5 in a 2:1:1 ratio / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Probable G-protein coupled receptor 158

MacromoleculeName: Probable G-protein coupled receptor 158 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.547109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGAMAYPLLL CLLLAQLGLG AVGASRDPQG RPDSPRERTP KGKPHAQQPG RASASDSSAP WSRSTDGTIL AQKLAEEVPM DVASYLYTG DSHQLKRANC SGRYELAGLP GKWPALASAH PSLHRALDTL THATNFLNVM LQSNKSREQN LQDDLDWYQA L VWSLLEGE ...String:
MGAMAYPLLL CLLLAQLGLG AVGASRDPQG RPDSPRERTP KGKPHAQQPG RASASDSSAP WSRSTDGTIL AQKLAEEVPM DVASYLYTG DSHQLKRANC SGRYELAGLP GKWPALASAH PSLHRALDTL THATNFLNVM LQSNKSREQN LQDDLDWYQA L VWSLLEGE PSISRAAITF STDSLSAPAP QVFLQATREE SRILLQDLSS SAPHLANATL ETEWFHGLRR KWRPHLHRRG PN QGPRGLG HSWRRKDGLG GDKSHFKWSP PYLECENGSY KPGWLVTLSS AIYGLQPNLV PEFRGVMKVD INLQKVDIDQ CSS DGWFSG THKCHLNNSE CMPIKGLGFV LGAYECICKA GFYHPGVLPV NNFRRRGPDQ HISGSTKDVS EEAYVCLPCR EGCP FCADD SPCFVQEDKY LRLAIISFQA LCMLLDFVSM LVVYHFRKAK SIRASGLILL ETILFGSLLL YFPVVILYFE PSTFR CILL RWARLLGFAT VYGTVTLKLH RVLKVFLSRT AQRIPYMTGG RVMRMLAVIL LVVFWFLIGW TSSVCQNLEK QISLIG QGK TSDHLIFNMC LIDRWDYMTA VAEFLFLLWG VYLCYAVRTV PSAFHEPRYM AVAVHNELII SAIFHTIRFV LASRLQS DW MLMLYFAHTH LTVTVTIGLL LIPKFSHSSN NPRDDIATEA YEDELDMGRS GSYLNSSINS AWSEHSLDPE DIRDELKK L YAQLEIYKRK KMITNNPHLQ KKRCSKKGLG RSIMRRITEI PETVSRQCSK EDKEGADHGT AKGTALIRKN PPESSGNTG KSKEETLKNR VFSLKKSHST YDHVRDQTEE SSSLPTESQE EETTENSTLE SLSGKKLTQK LKERGRLEVL FQGPGGSMSK GEELFTGVV PILVELDGDV NGHKFSVRGE GEGDATNGKL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKRHD F FKSAMPEG YVQERTISFK DDGTYKTRAE VKFEGDTLVN RIELKGIDFK EDGNILGHKL EYNFNSHNVY ITADKQKNGI KA NFKIRHN VEDGSVQLAD HYQQNTPIGD GPVLLPDNHY LSTQSVLSKD PNEKRDHMVL LEFVTAAGIT HGGSWSHPQF EKG GGSGGG SGGSAWSHPQ FE

UniProtKB: Metabotropic glycine receptor

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Macromolecule #2: Regulator of G-protein signaling 7

MacromoleculeName: Regulator of G-protein signaling 7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.570086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAQGNNYGQT SNGVADESPN MLVYRKMEDV IARMQDEKNG IPIRTVKSFL SKIPSVFSGS DIVQWLIKNL TIEDPVEALH LGTLMAAHG YFFPISDHVL TLKDDGTFYR FQTPYFWPSN CWEPENTDYA VYLCKRTMQN KARLELADYE AESLARLQRA F ARKWEFIF ...String:
MAQGNNYGQT SNGVADESPN MLVYRKMEDV IARMQDEKNG IPIRTVKSFL SKIPSVFSGS DIVQWLIKNL TIEDPVEALH LGTLMAAHG YFFPISDHVL TLKDDGTFYR FQTPYFWPSN CWEPENTDYA VYLCKRTMQN KARLELADYE AESLARLQRA F ARKWEFIF MQAEAQAKVD KKRDKIERKI LDSQERAFWD VHRPVPGCVN TTEVDIKKSS RMRNPHKTRK SVYGLQNDIR SH SPTHTPT PETKPPTEDE LQQQIKYWQI QLDRHRLKMS KVADSLLSYT EQYLEYDPFL LPPDPSNPWL SDDTTFWELE ASK EPSQQR VKRWGFGMDE ALKDPVGREQ FLKFLESEFS SENLRFWLAV EDLKKRPIKE VPSRVQEIWQ EFLAPGAPSA INLD SKSYD KTTQNVKEPG RYTFEDAQEH IYKLMKSDSY PRFIRSSAYQ ELLQAKKKSG NSMDRRTSFE KFAQNVGRNI PIFPC HKNC TPTLRASTNL LRGRGGSENL YFQGGSGSGG DYKDDDDKDY KDDDDK

UniProtKB: Regulator of G-protein signaling 7

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Macromolecule #3: Guanine nucleotide-binding protein subunit beta-5

MacromoleculeName: Guanine nucleotide-binding protein subunit beta-5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.619297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MCDQTFLVNV FGSCDKCFKQ RALRPVFKKS QQLSYCSTCA EIMATEGLHE NETLASLKSE AESLKGKLEE ERAKLHDVEL HQVAERVEA LGQFVMKTRR TLKGHGNKVL CMDWCKDKRR IVSSSQDGKV IVWDSFTTNK EHAVTMPCTW VMACAYAPSG C AIACGGLD ...String:
MCDQTFLVNV FGSCDKCFKQ RALRPVFKKS QQLSYCSTCA EIMATEGLHE NETLASLKSE AESLKGKLEE ERAKLHDVEL HQVAERVEA LGQFVMKTRR TLKGHGNKVL CMDWCKDKRR IVSSSQDGKV IVWDSFTTNK EHAVTMPCTW VMACAYAPSG C AIACGGLD NKCSVYPLTF DKNENMAAKK KSVAMHTNYL SACSFTNSDM QILTASGDGT CALWDVESGQ LLQSFHGHGA DV LCLDLAP SETGNTFVSG GCDKKAMVWD MRSGQCVQAF ETHESDINSV RYYPSGDAFA SGSDDATCRL YDLRADREVA IYS KESIIF GASSVDFSLS GRLLFAGYND YTINVWDVLK GSRVSILFGH ENRVSTLRVS PDGTAFCSGS WDHTLRVWA

UniProtKB: Guanine nucleotide-binding protein subunit beta-5

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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

Concentration4.5 mg/mL
BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 362999
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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