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- EMDB-31366: Locally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5... -

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Basic information

Entry
Database: EMDB / ID: EMD-31366
TitleLocally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5 in a 2:2:2 ratio
Map data
Sample
  • Complex: Locally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5 in a 2:2:2 ratio
    • Protein or peptide: GPR158
    • Protein or peptide: GPR158
    • 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 / light adaption / dark adaptation / 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 / light adaption / dark adaptation / 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 / negative regulation of G protein-coupled receptor signaling pathway / G protein-coupled dopamine receptor signaling pathway / regulation of synapse organization / parallel fiber to Purkinje cell synapse / G-protein alpha-subunit binding / response to amphetamine / enzyme activator activity / GTPase activator activity / positive regulation of GTPase activity / cell projection / protein localization to plasma membrane / 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 / transmembrane signaling receptor activity / 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 / 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 / response to ethanol / G alpha (q) signalling events / postsynaptic membrane / Extra-nuclear estrogen signaling / intracellular signal transduction / neuron projection / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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: 4.65 Å
AuthorsKim Y / Jeong E / Jeong J / Cho Y
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 26, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.439
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.439
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31366.png

Downloads & links

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Map

FileDownload / File: emd_31366.map.gz / Format: CCP4 / Size: 163.6 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 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: 0.439 / Movie #1: 0.439
Minimum - Maximum-1.9776472 - 4.6416078
Average (Standard dev.)-0.0015373251 (±0.033639517)
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
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-1.9784.642-0.002

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Supplemental data

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Sample components

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Entire : Locally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5...

EntireName: Locally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5 in a 2:2:2 ratio
Components
  • Complex: Locally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5 in a 2:2:2 ratio
    • Protein or peptide: GPR158
    • Protein or peptide: GPR158
    • 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: Locally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5...

SupramoleculeName: Locally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5 in a 2:2:2 ratio
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: GPR158

MacromoleculeName: GPR158 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 LKE RGRLEV LFQGPGGSMS KGEE LFTGV VPILVELDGD VNGHK FSVR GEGEGDATNG KLTLKF ICT TGKLPVPWPT LVTTLTY GV QCFSRYPDHM KRHDFFKS A MPEGYVQERT ISFKDDGTY KTRAEVKFEG DTLVNRIELK GIDFKEDGN ILGHKLEYNF N SHNVYITA DKQKNGIKAN FK IRHNVED GSVQLADHYQ QNT PIGDGP VLLPDNHYLS TQSV LSKDP NEKRDHMVLL EFVTA AGIT HGGSWSHPQF EKGGGS GGG SGGSAWSHPQ FE

GENBANK: GENBANK: Q5T848

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Macromolecule #2: GPR158

MacromoleculeName: GPR158 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 LKE RGRLEV LFQGPGGSMS KGEE LFTGV VPILVELDGD VNGHK FSVR GEGEGDATNG KLTLKF ICT TGKLPVPWPT LVTTLTY GV QCFSRYPDHM KRHDFFKS A MPEGYVQERT ISFKDDGTY KTRAEVKFEG DTLVNRIELK GIDFKEDGN ILGHKLEYNF N SHNVYITA DKQKNGIKAN FK IRHNVED GSVQLADHYQ QNT PIGDGP VLLPDNHYLS TQSV LSKDP NEKRDHMVLL EFVTA AGIT HGGSWSHPQF EKGGGS GGG SGGSAWSHPQ FE

GENBANK: GENBANK: Q5T848

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Macromolecule #3: Regulator of G-protein signaling 7

MacromoleculeName: Regulator of G-protein signaling 7 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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

GENBANK: GENBANK: P49802

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Macromolecule #4: Guanine nucleotide-binding protein subunit beta-5

MacromoleculeName: Guanine nucleotide-binding protein subunit beta-5 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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

GENBANK: GENBANK: O14775

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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
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: 4.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 236504
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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