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- EMDB-38527: Cryo-EM structure of Lys05 bound GPR30-Gq complex structure -

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Basic information

Entry
Database: EMDB / ID: EMD-38527
TitleCryo-EM structure of Lys05 bound GPR30-Gq complex structure
Map data
Sample
  • Complex: GPR30-Gq complex
    • Complex: GPR30-Gq
      • Protein or peptide: G protein subunit q
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: G-protein coupled estrogen receptor 1
    • Complex: Nanobody35
      • Protein or peptide: Nanobody35
  • Ligand: Lys01
KeywordsGPCR / estrogen / GPR30 / Gq / MEMBRANE PROTEIN / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of leukocyte activation / nuclear fragmentation involved in apoptotic nuclear change / positive regulation of cardiac vascular smooth muscle cell differentiation / negative regulation of cell cycle process / keratin filament / positive regulation of inositol trisphosphate biosynthetic process / positive regulation of uterine smooth muscle contraction / negative regulation of lipid biosynthetic process / apoptotic chromosome condensation / steroid hormone binding ...negative regulation of leukocyte activation / nuclear fragmentation involved in apoptotic nuclear change / positive regulation of cardiac vascular smooth muscle cell differentiation / negative regulation of cell cycle process / keratin filament / positive regulation of inositol trisphosphate biosynthetic process / positive regulation of uterine smooth muscle contraction / negative regulation of lipid biosynthetic process / apoptotic chromosome condensation / steroid hormone binding / cellular response to mineralocorticoid stimulus / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of endothelial cell apoptotic process / positive regulation of extrinsic apoptotic signaling pathway / dendritic spine membrane / cellular response to peptide hormone stimulus / positive regulation of neurotransmitter secretion / positive regulation of neurogenesis / positive regulation of epidermal growth factor receptor signaling pathway / G protein-coupled estrogen receptor activity / nuclear estrogen receptor activity / positive regulation of release of cytochrome c from mitochondria / : / negative regulation of fat cell differentiation / dendritic spine head / presynaptic active zone / negative regulation of vascular associated smooth muscle cell proliferation / steroid hormone receptor signaling pathway / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / neuronal action potential / nuclear receptor-mediated steroid hormone signaling pathway / axon terminus / regulation of cytosolic calcium ion concentration / steroid binding / hippocampal mossy fiber to CA3 synapse / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / cellular response to estradiol stimulus / G protein-coupled receptor activity / positive regulation of protein localization to plasma membrane / cellular response to glucose stimulus / mitochondrial membrane / trans-Golgi network / cytoplasmic vesicle membrane / positive regulation of insulin secretion / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / recycling endosome / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / negative regulation of ERK1 and ERK2 cascade / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / negative regulation of inflammatory response / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / vasodilation / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / cellular response to tumor necrosis factor / GTPase binding / nuclear envelope / retina development in camera-type eye / presynaptic membrane / nervous system development / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / fibroblast proliferation
Similarity search - Function
: / 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 / Guanine nucleotide-binding protein, beta subunit / G-protein, beta 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 / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
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 / G-protein coupled estrogen receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLiu H / Xu P / Xu HE
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2024
Title: Structural and functional evidence that GPR30 is not a direct estrogen receptor.
Authors: Heng Liu / Shimeng Guo / Antao Dai / Peiyu Xu / Xin Li / Sijie Huang / Xinheng He / Kai Wu / Xinyue Zhang / Dehua Yang / Xin Xie / H Eric Xu /
History
DepositionJan 1, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38527.png

Downloads & links

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Map

FileDownload / File: emd_38527.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 256 pix.
= 186.88 Å		0.73 Å/pix.
x 256 pix.
= 186.88 Å		0.73 Å/pix.
x 256 pix.
= 186.88 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.2400703 - 2.188374
Average (Standard dev.)0.0049087917 (±0.071607605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 186.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38527_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38527_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_38527_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : GPR30-Gq complex

EntireName: GPR30-Gq complex
Components
  • Complex: GPR30-Gq complex
    • Complex: GPR30-Gq
      • Protein or peptide: G protein subunit q
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: G-protein coupled estrogen receptor 1
    • Complex: Nanobody35
      • Protein or peptide: Nanobody35
  • Ligand: Lys01

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Supramolecule #1: GPR30-Gq complex

SupramoleculeName: GPR30-Gq complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: GPR30-Gq

SupramoleculeName: GPR30-Gq / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3, #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Nanobody35

SupramoleculeName: Nanobody35 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Lama glama (llama)

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Macromolecule #1: G protein subunit q

MacromoleculeName: G protein subunit q / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.632219 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RRTLRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RRTLRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTSGIFETK FQVDKVNFHM FDVGAQRDER RKWIQCFNDV TAIIFVVDSS DTNRLQEALN DF DSIWNNR WLRTISVILF LNKQDLLAEK VLAGKSKIED YFPEFARYTT PEDATPEPGE DPRVTRAKYF IRKEFVDIST ASG DGRHIC YPHFTCAVDT ENARRIFNDC KDIILQMNLR EYNLV

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Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.744371 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI ...String:
MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI VTSSGDTTCA LWDIETGQQT TTFTGHTGDV MSLSLAPDTR LFVSGACDAS AKLWDVREGM CRQTFTGHES DI NAICFFP NGNAFATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGYDDFNCNV WDALKADRAG VLA GHDNRV SCLGVTDDGM AVATGSWDSF LKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #4: Nanobody35

MacromoleculeName: Nanobody35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15.140742 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSSH HHHHHEPEA

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Macromolecule #5: G-protein coupled estrogen receptor 1

MacromoleculeName: G-protein coupled estrogen receptor 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.291457 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDVTSQARGV GLEMYPGTAQ PAAPNTTSPE LNLSHPLLGT ALANGTGELS EHQQYVIGLF LSCLYTIFLF PIGFVGNILI LVVNISFRE KMTIPDLYFI NLAVADLILV ADSLIEVFNL HERYYDIAVL CTFMSLFLQV NMYSSVFFLT WMSFDRYIAL A RAMRCSLF ...String:
MDVTSQARGV GLEMYPGTAQ PAAPNTTSPE LNLSHPLLGT ALANGTGELS EHQQYVIGLF LSCLYTIFLF PIGFVGNILI LVVNISFRE KMTIPDLYFI NLAVADLILV ADSLIEVFNL HERYYDIAVL CTFMSLFLQV NMYSSVFFLT WMSFDRYIAL A RAMRCSLF RTKHHARLSC GLIWMASVSA TLVPFTAVHL QHTDEACFCF ADVREVQWLE VTLGFIVPFA IIGLCYSLIV RV LVRAHRH RGLRPRRQKA LRMILAVVLV FFVCWLPENV FISVHLLQRT QPGAAPCKQS FRHAHPLTGH IVNLAAFSNS CLN PLIYSF LGETFRDKLR LYIEQKTNLP ALNRFCHAAL KAVIPDSTEQ SDVRFSSAV

UniProtKB: G-protein coupled estrogen receptor 1

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Macromolecule #6: Lys01

MacromoleculeName: Lys01 / type: ligand / ID: 6 / Number of copies: 1 / Formula: A1LVW
Molecular weightTheoretical: 440.368 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 209371
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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