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- EMDB-43236: Cryo-EM structure of GPR119-Gs-Nb35 complex with small molecule a... -

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Entry
Database: EMDB / ID: EMD-43236
TitleCryo-EM structure of GPR119-Gs-Nb35 complex with small molecule agonist MBX-2982
Map data
Sample
  • Complex: The complex of GPR119-Gs-Nb35 (composite map)
    • Complex: Glucose-dependent insulinotropic receptor
      • Protein or peptide: Soluble cytochrome b562,Glucose-dependent insulinotropic receptor,LgBiT
    • Complex: G-protein complex
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, HiBiT
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Complex: Nanobody35
      • Protein or peptide: Nanobody35
  • Ligand: 2-[1-(5-ethylpyrimidin-2-yl)piperidin-4-yl]-4-[[4-(1,2,3,4-tetrazol-1-yl)phenoxy]methyl]-1,3-thiazole
KeywordsCryoEM / GPCR / Orphan / G protein complex / Active / Agonist / MEMBRANE PROTEIN / Diabetes / native Mass Spectrometry / MEMBRANE PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / phosphatidylcholine binding / regulation of metabolic process / insulin secretion / PKA activation in glucagon signalling / hair follicle placode formation / developmental growth / D1 dopamine receptor binding / intracellular transport / renal water homeostasis ...Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / phosphatidylcholine binding / regulation of metabolic process / insulin secretion / PKA activation in glucagon signalling / hair follicle placode formation / developmental growth / D1 dopamine receptor binding / intracellular transport / renal water homeostasis / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / cellular response to glucagon stimulus / adenylate cyclase activator activity / regulation of insulin secretion / trans-Golgi network membrane / G protein-coupled receptor activity / negative regulation of inflammatory response to antigenic stimulus / electron transport chain / bone development / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / G protein activity / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / platelet aggregation / 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 / cognition / 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 / 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 / sensory perception of smell / 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 / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / fibroblast proliferation / G alpha (i) signalling events / 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 / receptor complex / iron ion binding / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / heme binding / synapse / protein-containing complex binding / GTP binding / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glucose-dependent insulinotropic receptor / Cytochrome b562 / Cytochrome b562 / G-protein alpha subunit, group S / Cytochrome c/b562 / 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 ...Glucose-dependent insulinotropic receptor / Cytochrome b562 / Cytochrome b562 / G-protein alpha subunit, group S / Cytochrome c/b562 / 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(s) subunit alpha isoforms short / Glucose-dependent insulinotropic receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Homo sapiens (human) / Lama glama (llama) / Oplophorus gracilirostris (crustacean)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsKim D-G / Cherezov V
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127086 United States
CitationJournal: To Be Published
Title: Native mass spectrometry prescreening of G protein-coupled receptor complexes for cryo-EM structure determination
Authors: Kim D-G / Liu W / Viner R / Cherezov V
History
DepositionJan 1, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43236.png

Downloads & links

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Map

FileDownload / File: emd_43236.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 324 pix.
= 298.08 Å		0.92 Å/pix.
x 324 pix.
= 298.08 Å		0.92 Å/pix.
x 324 pix.
= 298.08 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.7
Minimum - Maximum-6.4583015 - 10.483261000000001
Average (Standard dev.)-0.0025364342 (±0.22143449)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 298.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_43236_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43236_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43236_half_map_2.map
Projections & Slices
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Sample components

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Entire : The complex of GPR119-Gs-Nb35 (composite map)

EntireName: The complex of GPR119-Gs-Nb35 (composite map)
Components
  • Complex: The complex of GPR119-Gs-Nb35 (composite map)
    • Complex: Glucose-dependent insulinotropic receptor
      • Protein or peptide: Soluble cytochrome b562,Glucose-dependent insulinotropic receptor,LgBiT
    • Complex: G-protein complex
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, HiBiT
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Complex: Nanobody35
      • Protein or peptide: Nanobody35
  • Ligand: 2-[1-(5-ethylpyrimidin-2-yl)piperidin-4-yl]-4-[[4-(1,2,3,4-tetrazol-1-yl)phenoxy]methyl]-1,3-thiazole

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Supramolecule #1: The complex of GPR119-Gs-Nb35 (composite map)

SupramoleculeName: The complex of GPR119-Gs-Nb35 (composite map) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Molecular weightTheoretical: 177 KDa

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Supramolecule #2: Glucose-dependent insulinotropic receptor

SupramoleculeName: Glucose-dependent insulinotropic receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 67 KDa

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Supramolecule #3: G-protein complex

SupramoleculeName: G-protein complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2, #4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93 KDa

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Supramolecule #4: Nanobody35

SupramoleculeName: Nanobody35 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15 KDa

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Macromolecule #1: 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, HiBiT
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.039648 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String:
GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWNG SSGGGGSGGG GSSGVSGWRL FKKIS

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

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Macromolecule #2: 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: 2 / 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 #3: Nanobody35

MacromoleculeName: Nanobody35 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15.140742 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSSH HHHHHEPEA

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Macromolecule #4: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.683434 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKNTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE ...String:
MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKNTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE YQLIDCAQYF LDKIDVIKQA DYVPSDQDLL RCRVLTSGIF ETKFQVDKVN FHMFDVGAQR DERRKWIQCF ND VTAIIFV VASSSYNMVI REDNQTNRLQ AALKLFDSIW NNKWLRDTSV ILFLNKQDLL AEKVLAGKSK IEDYFPEFAR YTT PEDATP EPGEDPRVTR AKYFIRDEFL RISTASGDGR HYCYPHFTCA VDTENIRRVF NDCRDIIQRM HLRQYELL

UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

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Macromolecule #5: Soluble cytochrome b562,Glucose-dependent insulinotropic receptor...

MacromoleculeName: Soluble cytochrome b562,Glucose-dependent insulinotropic receptor,LgBiT
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oplophorus gracilirostris (crustacean)
Molecular weightTheoretical: 67.778492 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: PGADLEDNWE TLNDNLKVIE KADNAAQVKD ALTKMRAAAL DAQKATPPKL EDKSPDSPEM KDFRHGFDIL VGQIDDALKL ANEGKVKEA QAAAEQLKTT RNAYIQKYLG SPIMESSFSF GVILAVLASL IIATNTLVAV AVLLLIHKND GVSLCFTLNL A VADTLIGV ...String:
PGADLEDNWE TLNDNLKVIE KADNAAQVKD ALTKMRAAAL DAQKATPPKL EDKSPDSPEM KDFRHGFDIL VGQIDDALKL ANEGKVKEA QAAAEQLKTT RNAYIQKYLG SPIMESSFSF GVILAVLASL IIATNTLVAV AVLLLIHKND GVSLCFTLNL A VADTLIGV AISGLLTDQL SSPSRPTQKT LCSLRMAFVT SSAAASVLTV MLITFDRYLA IKQPFRYLKI MSGFVAGACI AG LWLVSYL IGFLPLGIPM FQQTAYKGQC SFFAVFHPHF VLTLSCVGFF PAMLLFVFFY CDMLKIASMH SQQIRKMEHA GAM AGGYRS PRTPSDFKAL RTVSVLIGSF ALSWTPFLIT GIVQVACQEC HLYLVLERYL WLLGVGNSLL NPLIYAYWQK EVRL QLYHM ALGVKKVLTS FLLFLSARNC GPERPRESSC HIVTISSSEF DGVFTLEDFV GDWEQTAAYN LDQVLEQGGV SSLLQ NLAV SVTPIQRIVR SGENALKIDI HVIIPYEGLS ADQMAQIEEV FKVVYPVDDH HFKVILPYGT LVIDGVTPNM LNYFGR PYE GIAVFDGKKI TVTGTLWNGN KIIDERLITP DGSMLFRVTI NSGGSLEVLF QG

UniProtKB: Soluble cytochrome b562, Glucose-dependent insulinotropic receptor

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Macromolecule #6: 2-[1-(5-ethylpyrimidin-2-yl)piperidin-4-yl]-4-[[4-(1,2,3,4-tetraz...

MacromoleculeName: 2-[1-(5-ethylpyrimidin-2-yl)piperidin-4-yl]-4-[[4-(1,2,3,4-tetrazol-1-yl)phenoxy]methyl]-1,3-thiazole
type: ligand / ID: 6 / Number of copies: 1 / Formula: 8VP
Molecular weightTheoretical: 448.544 Da
Chemical component information

ChemComp-8VP:
2-[1-(5-ethylpyrimidin-2-yl)piperidin-4-yl]-4-[[4-(1,2,3,4-tetrazol-1-yl)phenoxy]methyl]-1,3-thiazole

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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

Concentration3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Pressure: 0.00039000000000000005 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 396 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 57653
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7wcm


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8vhf:
Cryo-EM structure of GPR119-Gs-Nb35 complex with small molecule agonist MBX-2982

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