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- EMDB-36484: Cryo-EM structure of succinate receptor bound to cis-epoxysuccini... -

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Basic information

Entry
Database: EMDB / ID: EMD-36484
TitleCryo-EM structure of succinate receptor bound to cis-epoxysuccinic acid coupling to Gi
Map data
Sample
  • Complex: GPCR complex of succinate receptor
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • 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: Soluble cytochrome b562,Succinate receptor 1,Oplophorus-luciferin 2-monooxygenase catalytic subunit
    • Protein or peptide: scFv16
  • Ligand: (2R,3S)-oxirane-2,3-dicarboxylic acid
KeywordsComplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


Oplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / regulation of angiotensin metabolic process / renin secretion into blood stream / Class A/1 (Rhodopsin-like receptors) / positive regulation of chemotaxis / macrophage activation involved in immune response / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway ...Oplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / regulation of angiotensin metabolic process / renin secretion into blood stream / Class A/1 (Rhodopsin-like receptors) / positive regulation of chemotaxis / macrophage activation involved in immune response / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / cellular response to forskolin / energy homeostasis / regulation of mitotic spindle organization / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / bioluminescence / Regulation of insulin secretion / G protein-coupled receptor binding / G protein-coupled receptor activity / electron transport chain / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / 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 / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / response to peptide hormone / 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 / positive regulation of inflammatory response / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / response to calcium ion / 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 / cellular response to catecholamine stimulus / 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 / GDP binding / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / glucose homeostasis / retina development in camera-type eye / signaling receptor activity / Ca2+ pathway / cell cortex / phospholipase C-activating G protein-coupled receptor signaling pathway / midbody / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / periplasmic space / electron transfer activity / iron ion binding / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / heme binding / synapse / protein-containing complex binding / GTP binding / nucleolus / magnesium ion binding / signal transduction / extracellular exosome / extracellular region / nucleoplasm
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein alpha subunit, group I / Calycin / 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 ...Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein alpha subunit, group I / Calycin / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Soluble cytochrome b562 / 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(i) subunit alpha-1 / Succinate receptor 1 / Oplophorus-luciferin 2-monooxygenase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human) / Oplophorus gracilirostris (crustacean)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang TX / Tang WQ / Li FH / Wang JY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2024
Title: Molecular activation and G protein coupling selectivity of human succinate receptor SUCR1.
Authors: Tianxin Wang / Wenqin Tang / Xiaolei Zhu / Zhenyu Lv / Jiayan Chen / Yongze Li / Xiaoyu Sun / Haoyu Lv / Quanchang Gu / Fahui Li / Jiangyun Wang /
History
DepositionJun 12, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36484.png

Downloads & links

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Map

FileDownload / File: emd_36484.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 400 pix.
= 269.6 Å		0.67 Å/pix.
x 400 pix.
= 269.6 Å		0.67 Å/pix.
x 400 pix.
= 269.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.674 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.271586 - 2.486791
Average (Standard dev.)-0.00089041865 (±0.049372066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 269.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36484_msk_1.map
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Half map: #2

Fileemd_36484_half_map_1.map
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Half map: #1

Fileemd_36484_half_map_2.map
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Sample components

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Entire : GPCR complex of succinate receptor

EntireName: GPCR complex of succinate receptor
Components
  • Complex: GPCR complex of succinate receptor
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • 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: Soluble cytochrome b562,Succinate receptor 1,Oplophorus-luciferin 2-monooxygenase catalytic subunit
    • Protein or peptide: scFv16
  • Ligand: (2R,3S)-oxirane-2,3-dicarboxylic acid

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Supramolecule #1: GPCR complex of succinate receptor

SupramoleculeName: GPCR complex of succinate receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.415031 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGGQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCA TDTKNVQFVF DAVTDVIIKN NLKDCGLF

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1

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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: 41.055867 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 LKIWNGSSGG GGSGGGGSSG VSGWRLFKKI S

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: Soluble cytochrome b562,Succinate receptor 1,Oplophorus-luciferin...

MacromoleculeName: Soluble cytochrome b562,Succinate receptor 1,Oplophorus-luciferin 2-monooxygenase catalytic subunit
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: Oplophorus-luciferin 2-monooxygenase
Source (natural)Organism: Oplophorus gracilirostris (crustacean)
Molecular weightTheoretical: 75.122805 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAGRAHHH HHHHHHHENL YFQSGAPADL EDNWETLNDN LKVIEKADNA AQVKDALTKM RAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQI DDALKLANEG KVKEAQAAAE QLKTTRNAYI QKYLLEVLFQ G PEFMLGIM ...String:
MKTIIALSYI FCLVFADYKD DDDAGRAHHH HHHHHHHENL YFQSGAPADL EDNWETLNDN LKVIEKADNA AQVKDALTKM RAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQI DDALKLANEG KVKEAQAAAE QLKTTRNAYI QKYLLEVLFQ G PEFMLGIM AWNATCKNWL AAEAALEKYY LSIFYGIEFV VGVLGNTIVV FGYLFCLKNW NSSNIYLFNL SISDLAFLCT LP MLIRSYA NGNWIYGDVL CISNRYVLHA NLYTSILFLT FISIDRYLII KYPFREHLLQ KKEFAILISL AIWVLVTLEL LPI LPLINP VITDNGTTCN DYASSGDPNY NLIYSMCLTL LGFLIPLFVM CFFYYKIALF LKQRNRQLAT ALPLEKPLNL VIMA VVIFS VLFTPYHVMR NVRIASRLGS WKQYQCTQVV INSFYIVTRP LAFLNSVINP VFYFLLGDHF REMLMNKLRH NFKSL TSFR RWAHELLLSF REKAAAVFTL EDFVGDWEQT AAYNLDQVLE QGGVSSLLQN LAVSVTPIQR IVRSGENALK IDIHVI IPY EGLSADQMAQ IEEVFKVVYP VDDHHFKVIL PYGTLVIDGV TPNMLNYFGR PYEGIAVFDG KKITVTGTLW NGNKIID ER LITPDGSMLF RVTINS

UniProtKB: Soluble cytochrome b562, Succinate receptor 1, Oplophorus-luciferin 2-monooxygenase catalytic subunit

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Macromolecule #5: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.668211 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSAIVLYVL LAAAAHSAFA DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFT ISRDDPKNTL FLQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV M TQATSSVP ...String:
MVSAIVLYVL LAAAAHSAFA DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFT ISRDDPKNTL FLQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV M TQATSSVP VTPGESVSIS CRSSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LE AEDVGVY YCMQHLEYPL TFGAGTKLEL KAAAENLYFQ SHHHHHHHH

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Macromolecule #6: (2R,3S)-oxirane-2,3-dicarboxylic acid

MacromoleculeName: (2R,3S)-oxirane-2,3-dicarboxylic acid / type: ligand / ID: 6 / Number of copies: 1 / Formula: U9S
Molecular weightTheoretical: 132.072 Da
Chemical component information

ChemComp-U9S:
(2R,3S)-oxirane-2,3-dicarboxylic acid

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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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 278158
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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