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- PDB-9ycx: Neurotensin Receptor 1 (NTSR1) bound to Octotensin in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9ycx
TitleNeurotensin Receptor 1 (NTSR1) bound to Octotensin in complex with Gi3 in the Non-Canonical Orientation
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Neurotensin receptor type 1
  • Tachykinin-1
  • scFv16
KeywordsMEMBRANE PROTEIN / Complex / Agonist
Function / homology
Function and homology information


G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / positive regulation of locomotion / regulation of inositol trisphosphate biosynthetic process / positive regulation of gamma-aminobutyric acid secretion / L-glutamate import across plasma membrane / D-aspartate import across plasma membrane / negative regulation of adenylate cyclase activity / positive regulation of arachidonate secretion ...G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / positive regulation of locomotion / regulation of inositol trisphosphate biosynthetic process / positive regulation of gamma-aminobutyric acid secretion / L-glutamate import across plasma membrane / D-aspartate import across plasma membrane / negative regulation of adenylate cyclase activity / positive regulation of arachidonate secretion / vocalization behavior / regulation of behavioral fear response / cAMP biosynthetic process / regulation of respiratory gaseous exchange / negative regulation of systemic arterial blood pressure / positive regulation of inhibitory postsynaptic potential / GTP metabolic process / negative regulation of release of sequestered calcium ion into cytosol / response to food / positive regulation of glutamate secretion / response to lipid / temperature homeostasis / regulation of membrane depolarization / positive regulation of inositol phosphate biosynthetic process / response to stress / positive regulation of macroautophagy / detection of temperature stimulus involved in sensory perception of pain / conditioned place preference / Adenylate cyclase inhibitory pathway / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / dendritic shaft / neuropeptide signaling pathway / G protein-coupled receptor binding / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / terminal bouton / G protein-coupled acetylcholine receptor signaling pathway / 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 / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / GDP binding / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / G beta:gamma signalling through BTK / 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 / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADP signalling through P2Y purinoceptor 1 / cellular response to catecholamine stimulus / G beta:gamma signalling through PI3Kgamma / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / 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 / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / ciliary basal body / GTPase binding / midbody / chemical synaptic transmission / Ca2+ pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / dendritic spine / G alpha (s) signalling events / G alpha (q) signalling events / cell division / cytoplasmic side of plasma membrane / perikaryon / Ras protein signal transduction / Extra-nuclear estrogen signaling / positive regulation of apoptotic process / membrane raft / G protein-coupled receptor signaling pathway / lysosomal membrane / centrosome / positive regulation of gene expression / GTPase activity / negative regulation of apoptotic process
Similarity search - Function
Tachykinin/Neurokinin-like, conserved site / Tachykinin family signature. / Neurotensin receptor / Neurotensin type 1 receptor / G-protein alpha subunit, group I / 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. ...Tachykinin/Neurokinin-like, conserved site / Tachykinin family signature. / Neurotensin receptor / Neurotensin type 1 receptor / G-protein alpha subunit, group I / 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 / Guanine nucleotide-binding protein, beta subunit / G protein beta WD-40 repeat protein / 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
Guanine nucleotide-binding protein G(i) subunit alpha-3 / Neurotensin receptor type 1 / 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 / Tachykinin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Octopus vulgaris (common octopus)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsRobertson, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT) United States
CitationJournal: To Be Published
Title: Prey-specific toxins provide broad venom activity in cephalopods
Authors: Koch, L.T. / Yeung, H.Y. / Torres, J.P. / Brandt, Z. / Palomino, S. / Ramiro, I.B.L. / Acyatan, Z. / Schumann, N. / Vo, A.A. / Chase, K. / Engholm, E. / Jensen, K.J. / Hansen, L.H. / ...Authors: Koch, L.T. / Yeung, H.Y. / Torres, J.P. / Brandt, Z. / Palomino, S. / Ramiro, I.B.L. / Acyatan, Z. / Schumann, N. / Vo, A.A. / Chase, K. / Engholm, E. / Jensen, K.J. / Hansen, L.H. / Peterson, R.T. / Robertson, M.J. / Ptwardhan, A. / Schjoldager, K.T. / Safavi-Hemami, H.
History
DepositionSep 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
L: Tachykinin-1
R: Neurotensin receptor type 1
A: Guanine nucleotide-binding protein G(i) subunit alpha-3
S: scFv16


Theoretical massNumber of molelcules
Total (without water)164,9476
Polymers164,9476
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules BCA

#1: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37671.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768
#5: Protein Guanine nucleotide-binding protein G(i) subunit alpha-3 / G(i) alpha-3


Mass: 40584.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08754

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Protein/peptide / Protein / Antibody , 3 types, 3 molecules LRS

#3: Protein/peptide Tachykinin-1 / OctTK-I / Tachykinin I


Mass: 1514.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Octopus vulgaris (common octopus) / Production host: synthetic construct (others) / References: UniProt: Q8I6S3
#4: Protein Neurotensin receptor type 1 / NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH


Mass: 49530.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTSR1, NTRR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30989
#6: Antibody scFv16


Mass: 27784.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Neurotensin-G protein complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 921595 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038795
ELECTRON MICROSCOPYf_angle_d0.55411985
ELECTRON MICROSCOPYf_dihedral_angle_d4.5071242
ELECTRON MICROSCOPYf_chiral_restr0.0431398
ELECTRON MICROSCOPYf_plane_restr0.0041519

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