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- EMDB-20836: neurotensin receptor and arrestin2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20836
Titleneurotensin receptor and arrestin2 complex
Map data
Sample
  • Complex: NTSR_Arrestin
    • Protein or peptide: ARG-ARG-PRO-TYR-ILE-LEU
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Neurotensin receptor type 1
    • Protein or peptide: unidentified peptide
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
KeywordsGPCR signaling / MEMBRANE PROTEIN
Function / homology
Function and homology information


neuropeptide receptor binding / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / angiotensin receptor binding / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / TGFBR3 regulates TGF-beta signaling / Activation of SMO / regulation of membrane depolarization ...neuropeptide receptor binding / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / angiotensin receptor binding / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / TGFBR3 regulates TGF-beta signaling / Activation of SMO / regulation of membrane depolarization / positive regulation of arachidonate secretion / negative regulation of interleukin-8 production / L-glutamate import across plasma membrane / regulation of respiratory gaseous exchange / neuropeptide hormone activity / positive regulation of inhibitory postsynaptic potential / G protein-coupled receptor internalization / arrestin family protein binding / negative regulation of systemic arterial blood pressure / negative regulation of release of sequestered calcium ion into cytosol / positive regulation of glutamate secretion / Lysosome Vesicle Biogenesis / negative regulation of NF-kappaB transcription factor activity / temperature homeostasis / positive regulation of inositol phosphate biosynthetic process / positive regulation of cardiac muscle hypertrophy / stress fiber assembly / Golgi Associated Vesicle Biogenesis / response to lipid / positive regulation of Rho protein signal transduction / pseudopodium / detection of temperature stimulus involved in sensory perception of pain / negative regulation of interleukin-6 production / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / enzyme inhibitor activity / neuropeptide signaling pathway / transport vesicle / insulin-like growth factor receptor binding / clathrin-coated pit / axon terminus / negative regulation of protein ubiquitination / GTPase activator activity / cytoplasmic vesicle membrane / Activated NOTCH1 Transmits Signal to the Nucleus / Peptide ligand-binding receptors / blood vessel diameter maintenance / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / adult locomotory behavior / learning / G protein-coupled receptor binding / Signaling by high-kinase activity BRAF mutants / G protein-coupled receptor activity / MAP2K and MAPK activation / cytoplasmic side of plasma membrane / positive regulation of protein phosphorylation / terminal bouton / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / Cargo recognition for clathrin-mediated endocytosis / protein transport / Thrombin signalling through proteinase activated receptors (PARs) / Clathrin-mediated endocytosis / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / perikaryon / G alpha (s) signalling events / G alpha (q) signalling events / molecular adaptor activity / chemical synaptic transmission / dendritic spine / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Ub-specific processing proteases / protein ubiquitination / nuclear body / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / membrane raft / receptor ligand activity / Golgi membrane / negative regulation of gene expression / lysosomal membrane / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / protein-containing complex binding / cell surface / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / Neurotensin receptor / Neurotensin type 1 receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain ...Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / Neurotensin receptor / Neurotensin type 1 receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / 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) / Immunoglobulin E-set
Similarity search - Domain/homology
Neurotensin receptor type 1 / Neurotensin/neuromedin N / Beta-arrestin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsQu QH / Huang W / Masureel M / Janetzko J / Kobilka BK / Skiniotis G
CitationJournal: Nature / Year: 2020
Title: Structure of the neurotensin receptor 1 in complex with β-arrestin 1.
Authors: Weijiao Huang / Matthieu Masureel / Qianhui Qu / John Janetzko / Asuka Inoue / Hideaki E Kato / Michael J Robertson / Khanh C Nguyen / Jeffrey S Glenn / Georgios Skiniotis / Brian K Kobilka /
Abstract: Arrestin proteins bind to active, phosphorylated G-protein-coupled receptors (GPCRs), thereby preventing G-protein coupling, triggering receptor internalization and affecting various downstream ...Arrestin proteins bind to active, phosphorylated G-protein-coupled receptors (GPCRs), thereby preventing G-protein coupling, triggering receptor internalization and affecting various downstream signalling pathways. Although there is a wealth of structural information detailing the interactions between GPCRs and G proteins, less is known about how arrestins engage GPCRs. Here we report a cryo-electron microscopy structure of full-length human neurotensin receptor 1 (NTSR1) in complex with truncated human β-arrestin 1 (βarr1(ΔCT)). We find that phosphorylation of NTSR1 is critical for the formation of a stable complex with βarr1(ΔCT), and identify phosphorylated sites in both the third intracellular loop and the C terminus that may promote this interaction. In addition, we observe a phosphatidylinositol-4,5-bisphosphate molecule forming a bridge between the membrane side of NTSR1 transmembrane segments 1 and 4 and the C-lobe of arrestin. Compared with a structure of a rhodopsin-arrestin-1 complex, in our structure arrestin is rotated by approximately 85° relative to the receptor. These findings highlight both conserved aspects and plasticity among arrestin-receptor interactions.
History
DepositionOct 16, 2019-
Header (metadata) releaseNov 6, 2019-
Map releaseFeb 26, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6up7
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20836.png

Downloads & links

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Map

FileDownload / File: emd_20836.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.05075385 - 0.078466654
Average (Standard dev.)0.00015428166 (±0.0020462896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 233.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z233.200233.200233.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0510.0780.000

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Supplemental data

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Sample components

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Entire : NTSR_Arrestin

EntireName: NTSR_Arrestin
Components
  • Complex: NTSR_Arrestin
    • Protein or peptide: ARG-ARG-PRO-TYR-ILE-LEU
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Neurotensin receptor type 1
    • Protein or peptide: unidentified peptide
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

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Supramolecule #1: NTSR_Arrestin

SupramoleculeName: NTSR_Arrestin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ARG-ARG-PRO-TYR-ILE-LEU

MacromoleculeName: ARG-ARG-PRO-TYR-ILE-LEU / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 819.007 Da
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
RRPYIL

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Macromolecule #2: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.06284 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: VFKKASPNGK LTVYLGKRDF VDHIDLVDPV DGVVLVDPEY LKERRVYVTL TVAFRYGRED LDVLGLTFRK DLFVANVQSF PPAPEDKKP LTRLQERLIK KLGEHAYPFT FEIPPNLPSS VTLQPGPEDT GKALGVDYEV KAFVAENLEE KIHKRNSVRL V IRKVQYAP ...String:
VFKKASPNGK LTVYLGKRDF VDHIDLVDPV DGVVLVDPEY LKERRVYVTL TVAFRYGRED LDVLGLTFRK DLFVANVQSF PPAPEDKKP LTRLQERLIK KLGEHAYPFT FEIPPNLPSS VTLQPGPEDT GKALGVDYEV KAFVAENLEE KIHKRNSVRL V IRKVQYAP ERPGPQPTAE TTRQFLMSDK PLHLEASLDK EIYYHGEPIS VNVHVTNNTN KTVKKIKISV RQYADIVLFN TA QYKVPVA MEEADDTVAP SSTFSKVYTL TPFLANNREK RGLALDGKLK HEDTNLASST LLREGANREI LGIIVSYKVK VKL VVSRGG LLGDLASSDV AVELPFTLMH PK

UniProtKB: Beta-arrestin-1

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Macromolecule #3: Neurotensin receptor type 1

MacromoleculeName: Neurotensin receptor type 1 / type: protein_or_peptide / ID: 3
Details: missing regions were not modeled due to local low resolution/flexibility.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.360656 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: PSSELDVNTD IYSKVLVTAV YLALFVVGTV GNTVTAFTLA RKKSLQSLQS TVHYHLGSLA LSDLLTLLLA MPVELYNFIW VHHPWAFGD AGCRGYYFLR DACTYATALN VASLSVERYL AICHPFKAKT LMSRSRTKKF ISAIWLASAL LAVPMLFTMG E QNRSADGQ ...String:
PSSELDVNTD IYSKVLVTAV YLALFVVGTV GNTVTAFTLA RKKSLQSLQS TVHYHLGSLA LSDLLTLLLA MPVELYNFIW VHHPWAFGD AGCRGYYFLR DACTYATALN VASLSVERYL AICHPFKAKT LMSRSRTKKF ISAIWLASAL LAVPMLFTMG E QNRSADGQ HAGGLVCTPT IHTATVKVVI QVNTFMSFIF PMVVISVLNT IIANKLTVMV RQAAEQGQVC TVGGEHSTFS MA IEPGRVQ ALRHGVRVLR AVVIAFVVCW LPYHVRRLMF CYISDEQWTP FLYDFYHYFY MVTNALFYVS STINPILYNL VSA NFRHIF LATLACLC

UniProtKB: Neurotensin receptor type 1

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Macromolecule #4: unidentified peptide

MacromoleculeName: unidentified peptide / type: protein_or_peptide / ID: 4
Details: actual sequence for this poly-A exists, however, the local resolution for this region is not sufficient to register the amino acids.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 783.958 Da
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #5: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
type: ligand / ID: 5 / Number of copies: 1 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-PIO:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

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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: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 254725
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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