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- EMDB-64907: Cryo-EM structure of human Neurotensin Receptor 1 (hNTSR1)-Gq (de... -

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Entry
Database: EMDB / ID: EMD-64907
TitleCryo-EM structure of human Neurotensin Receptor 1 (hNTSR1)-Gq (delipidated) complex in nucleotide-free C state
Map data
Sample
  • Complex: JMV449-bound human Neurotensin Receptor 1 (hNTSR1)-GqiN18 complex in nucleotide-free C state with scFv16
    • Complex: JMV449-bound human neurotensin receptor type 1
      • Protein or peptide: Neurotensin receptor type 1
      • Protein or peptide: JMV449
    • Complex: heterotrimeric GqiN18 protein with delipidation mutations
      • Protein or peptide: Guanine nucleotide-binding protein G(q) subunit alpha
      • 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
    • Complex: scFv16
      • Protein or peptide: scFv16
  • Ligand: water
KeywordsGPCR / NTSR1 / neurotensin / G-protein / membrane protein
Function / homology
Function and homology information


Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / G protein-coupled neurotensin receptor activity / sensory perception of itch / inositol phosphate catabolic process / symmetric synapse / positive regulation of locomotion / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / regulation of inositol trisphosphate biosynthetic process / PLC beta mediated events ...Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / G protein-coupled neurotensin receptor activity / sensory perception of itch / inositol phosphate catabolic process / symmetric synapse / positive regulation of locomotion / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / regulation of inositol trisphosphate biosynthetic process / PLC beta mediated events / phospholipase C-activating serotonin receptor signaling pathway / regulation of platelet activation / entrainment of circadian clock / positive regulation of gamma-aminobutyric acid secretion / D-aspartate import across plasma membrane / positive regulation of arachidonate secretion / L-glutamate import across plasma membrane / vocalization behavior / regulation of behavioral fear response / cAMP biosynthetic process / regulation of respiratory gaseous exchange / positive regulation of inhibitory postsynaptic potential / negative regulation of systemic arterial blood pressure / regulation of canonical Wnt signaling pathway / negative regulation of release of sequestered calcium ion into cytosol / glutamate receptor signaling pathway / mast cell degranulation / positive regulation of glutamate secretion / response to food / regulation of membrane depolarization / response to lipid / temperature homeostasis / positive regulation of inositol phosphate biosynthetic process / detection of temperature stimulus involved in sensory perception of pain / response to stress / phototransduction, visible light / photoreceptor outer segment / postsynaptic cytosol / conditioned place preference / cellular response to acidic pH / hormone-mediated signaling pathway / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / GTPase activator activity / dendritic shaft / adult locomotory behavior / neuropeptide signaling pathway / response to prostaglandin E / G protein-coupled receptor binding / G protein-coupled receptor activity / cytoplasmic side of plasma membrane / G-protein beta/gamma-subunit complex binding / blood coagulation / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / terminal bouton / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G beta:gamma signalling through BTK / photoreceptor disc membrane / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / 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 / heterotrimeric G-protein complex / G alpha (12/13) signalling events / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / extracellular vesicle / sensory perception of taste / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / retina development in camera-type eye / GTPase binding / fibroblast proliferation / G protein activity / Ca2+ pathway / nuclear membrane
Similarity search - Function
G-protein alpha subunit, group Q / Neurotensin receptor / Neurotensin type 1 receptor / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit / G-protein gamma subunit domain profile. ...G-protein alpha subunit, group Q / Neurotensin receptor / Neurotensin type 1 receptor / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / 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 / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 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. / 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
Neurotensin receptor type 1 / Guanine nucleotide-binding protein G(q) subunit alpha / 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
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others) / Mus musculus (house mouse)
Methodsingle particle reconstruction / Resolution: 2.24 Å
AuthorsMatsui TE / Kobayashi K / Fukuda M / Kawakami K / Yamashita K / Kato HE
Funding support Japan, 7 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25K09525 Japan
Japan Society for the Promotion of Science (JSPS)24H02262 Japan
Japan Society for the Promotion of Science (JSPS)25H01338 Japan
Japan Society for the Promotion of Science (JSPS)24KJ0981 Japan
Japan Society for the Promotion of Science (JSPS)25H02243 Japan
Japan Society for the Promotion of Science (JSPS)24K18060 Japan
Japan Society for the Promotion of Science (JSPS)23KJ0363 Japan
CitationJournal: Nature / Year: 2026
Title: The dynamic basis of G-protein recognition and activation by a GPCR.
Authors: Kazuhiro Kobayashi / Kouki Kawakami / Toshiki E Matsui / Shun Yokoi / Masahiro Fukuda / Tomohiro J Narita / Hiroki Arai / Mai Tambo / Takashi Sumikama / Manae Tatsumi / Keitaro Yamashita / ...Authors: Kazuhiro Kobayashi / Kouki Kawakami / Toshiki E Matsui / Shun Yokoi / Masahiro Fukuda / Tomohiro J Narita / Hiroki Arai / Mai Tambo / Takashi Sumikama / Manae Tatsumi / Keitaro Yamashita / Junki Koyanagi / Mai Kugawa / Hisako Ikeda / Ayumi Sumino / Ayori Mitsutake / Brian K Kobilka / Asuka Inoue / Hideaki E Kato /
Abstract: G-protein-coupled receptor (GPCR) signalling occurs through heterotrimeric G proteins, whose selective activation leads to distinct cellular outcomes. Although more than 200 GPCR-G protein complex ...G-protein-coupled receptor (GPCR) signalling occurs through heterotrimeric G proteins, whose selective activation leads to distinct cellular outcomes. Although more than 200 GPCR-G protein complex structures have been determined, these static snapshots provide limited insight into the dynamics of G-protein association and dissociation. Here we present cryo-electron microscopy structures of human neurotensin receptor type 1 (NTSR1) with minimally modified G and G, showing how the receptor's intracellular surface dynamically rearranges to accommodate each G-protein subtype. Furthermore, time-resolved cryo-electron microscopy analyses of NTSR1-G visualized G-protein dissociation processes on GDP/GTP binding. Characterization of more than 20 intermediates, complemented by mutational and computational analyses, identifies four key mechanistic features. First, GDP/GTP induces G release from both canonical and non-canonical active conformations with distinct kinetics. Second, NTSR1 uses common intracellular rearrangements to recognize different G-protein subtypes and to promote activation of a single subtype. Third, separation from Gβγ involves stepwise remodelling of the Gα switches I-III. Finally, G dissociates from the receptor through a pathway that is distinct from that of G, and the canonical and non-canonical NTSR1-G complexes further diverge in their dissociation trajectories. These findings provide a comprehensive framework for understanding GPCR signalling dynamics and guiding signal-targeted therapeutic development.
History
DepositionJun 4, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64907.png

Downloads & links

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Map

FileDownload / File: emd_64907.map.gz / Format: CCP4 / Size: 16.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 164 pix.
= 173.84 Å		1.06 Å/pix.
x 164 pix.
= 173.84 Å		1.06 Å/pix.
x 164 pix.
= 173.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0025
Minimum - Maximum-0.034679983 - 0.09486931
Average (Standard dev.)-0.00020256717 (±0.004540366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions164164164
Spacing164164164
CellA=B=C: 173.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64907_msk_1.map
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Half map: #2

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Sample components

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Entire : JMV449-bound human Neurotensin Receptor 1 (hNTSR1)-GqiN18 complex...

EntireName: JMV449-bound human Neurotensin Receptor 1 (hNTSR1)-GqiN18 complex in nucleotide-free C state with scFv16
Components
  • Complex: JMV449-bound human Neurotensin Receptor 1 (hNTSR1)-GqiN18 complex in nucleotide-free C state with scFv16
    • Complex: JMV449-bound human neurotensin receptor type 1
      • Protein or peptide: Neurotensin receptor type 1
      • Protein or peptide: JMV449
    • Complex: heterotrimeric GqiN18 protein with delipidation mutations
      • Protein or peptide: Guanine nucleotide-binding protein G(q) subunit alpha
      • 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
    • Complex: scFv16
      • Protein or peptide: scFv16
  • Ligand: water

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Supramolecule #1: JMV449-bound human Neurotensin Receptor 1 (hNTSR1)-GqiN18 complex...

SupramoleculeName: JMV449-bound human Neurotensin Receptor 1 (hNTSR1)-GqiN18 complex in nucleotide-free C state with scFv16
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: JMV449-bound human neurotensin receptor type 1

SupramoleculeName: JMV449-bound human neurotensin receptor type 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: heterotrimeric GqiN18 protein with delipidation mutations

SupramoleculeName: heterotrimeric GqiN18 protein with delipidation mutations
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: scFv16

SupramoleculeName: scFv16 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6

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Macromolecule #1: Neurotensin receptor type 1

MacromoleculeName: Neurotensin receptor type 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.535051 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGQPGNGSAF LLAPNRSHAP DHDVENLYFQ GQRAQAGLEE ALLAPGFGNA SGNASERVLA APSSELDVNT DIYSKVLVTA VYLALFVVG TVGNTVTLFT LARKKSLQSL QSTVHYHLGS LALSDLLTLL LAMPVELYNF IWVHHPWAFG DAGCRGYYFL R DACTYATA ...String:
MGQPGNGSAF LLAPNRSHAP DHDVENLYFQ GQRAQAGLEE ALLAPGFGNA SGNASERVLA APSSELDVNT DIYSKVLVTA VYLALFVVG TVGNTVTLFT LARKKSLQSL QSTVHYHLGS LALSDLLTLL LAMPVELYNF IWVHHPWAFG DAGCRGYYFL R DACTYATA LNVASLSVER YLAICHPFKA KTLMSRSRTK KFISAIWLAS ALLAVPMLFT MGEQNRSADG QHAGGLVCTP TI HTATVKV VIQVNTFMSF IFPMVVISVL NTIIANKLTV MVRQAAEQGQ VCTVGGEHST FSMAIEPGRV QALRHGVRVL RAV VIAFVV CWLPYHVRRL MFCYISDEQW TPFLYDFYHY FYMVTNALFY VSSTINPILY NLVSANFRHI FLATLACLCP VWRR RRKRP AFSRKADSVS SNHTLSSNAT RETLYLEVLF Q

UniProtKB: Neurotensin receptor type 1

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Macromolecule #2: JMV449

MacromoleculeName: JMV449 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 762.979 Da
SequenceString:
KKPYIL

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Macromolecule #3: Guanine nucleotide-binding protein G(q) subunit alpha

MacromoleculeName: Guanine nucleotide-binding protein G(q) subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.365066 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSTLSAEDK AAVERSKMIE RQLRRDKRDA RRELKLLLLG TGESGKSTFI KQMRIIHGSG YSDEDKRGFT KLVYQNIFTA MQAMIRAMD TLKIPYKYEH NKAHAQLVRE VDVEKVSAFE NPYVDAIKSL WNDPGIQECY DRRREYQLSD STKYYLNDLD R VADPAYLP ...String:
MGSTLSAEDK AAVERSKMIE RQLRRDKRDA RRELKLLLLG TGESGKSTFI KQMRIIHGSG YSDEDKRGFT KLVYQNIFTA MQAMIRAMD TLKIPYKYEH NKAHAQLVRE VDVEKVSAFE NPYVDAIKSL WNDPGIQECY DRRREYQLSD STKYYLNDLD R VADPAYLP TQQDVLRVRV PTTGIIEYPF DLQSVIFRMV DVGGQRSERR KWIHCFENVT SIMFLVALSE YDQVLVESDN EN RMEESKA LFRTIITYPW FQNSSVILFL NKKDLLEEKI MYSHLVDYFP EYDGPQRDAQ AAREFILKMF VDLNPDSDKI IYS HFTCAT DTENIRFVFA AVKDTILQLN LKEYNLV

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

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Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.430137 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR ...String:
MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR FLDDNQIVIS SGDTTCALWD IETGQQTTTF TGHTGDVMSL SLAPDTRLFV SGACDASAKL WDVREGMCRQ TF TGHESDI NAICFFPNGN AFATGSDDAT CRLFDLRADQ ELMTYSHDNI ICGITSVSFS KSGRLLLAGY DDFNCNVWDA LKA DRAGVL AGHDNRVSCL GVTDDGMAVA TGSWDSFLKI WN

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

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Macromolecule #5: 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: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.845078 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFSAI L

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

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Macromolecule #6: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.784896 KDa
Recombinant expressionOrganism: Trichoplusia ni ascovirus 2a
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KAAAHHHHHH HH

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 205 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6os9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1092577
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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