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- PDB-6up7: neurotensin receptor and arrestin2 complex -

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Basic information

Entry
Database: PDB / ID: 6up7
Titleneurotensin receptor and arrestin2 complex
Components
  • ARG-ARG-PRO-TYR-ILE-LEU
  • Beta-arrestin-1Arrestin
  • Neurotensin receptor type 1
  • unidentified peptide
KeywordsMEMBRANE PROTEIN / GPCR signaling
Function / homology
Function and homology information


neuropeptide receptor binding / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / angiotensin receptor binding / positive regulation of inhibitory postsynaptic potential / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / Activation of SMO / negative regulation of interleukin-8 production ...neuropeptide receptor binding / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / angiotensin receptor binding / positive regulation of inhibitory postsynaptic potential / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / Activation of SMO / negative regulation of interleukin-8 production / L-glutamate import across plasma membrane / positive regulation of arachidonic acid secretion / regulation of respiratory gaseous exchange / neuropeptide hormone activity / negative regulation of systemic arterial blood pressure / arrestin family protein binding / G protein-coupled receptor internalization / negative regulation of release of sequestered calcium ion into cytosol / enzyme inhibitor activity / positive regulation of glutamate secretion / positive regulation of inositol phosphate biosynthetic process / temperature homeostasis / Lysosome Vesicle Biogenesis / positive regulation of Rho protein signal transduction / Golgi Associated Vesicle Biogenesis / response to lipid / negative regulation of NF-kappaB transcription factor activity / stress fiber assembly / regulation of membrane depolarization / negative regulation of Notch signaling pathway / pseudopodium / detection of temperature stimulus involved in sensory perception of pain / negative regulation of interleukin-6 production / positive regulation of receptor internalization / neuropeptide signaling pathway / axon terminus / clathrin-coated pit / negative regulation of protein ubiquitination / transport vesicle / insulin-like growth factor receptor binding / visual perception / Activated NOTCH1 Transmits Signal to the Nucleus / blood vessel diameter maintenance / GTPase activator activity / Peptide ligand-binding receptors / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / learning / G protein-coupled receptor binding / G protein-coupled receptor activity / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cytoplasmic vesicle membrane / terminal bouton / cytoplasmic side of plasma membrane / 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 / Signaling by BRAF and RAF1 fusions / Thrombin signalling through proteinase activated receptors (PARs) / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of NF-kappaB transcription factor activity / ubiquitin-dependent protein catabolic process / perikaryon / chemical synaptic transmission / cytoplasmic vesicle / G alpha (s) signalling events / G alpha (q) signalling events / proteasome-mediated ubiquitin-dependent protein catabolic process / dendritic spine / transcription coactivator activity / receptor ligand activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / nuclear body / Ub-specific processing proteases / positive regulation of protein phosphorylation / positive regulation of apoptotic process / membrane raft / G protein-coupled receptor signaling pathway / lysosomal membrane / Golgi membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / chromatin / protein-containing complex binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II
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
Chem-PIO / Neurotensin receptor type 1 / Neurotensin/neuromedin N / Beta-arrestin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsQu, Q.H. / Huang, W. / Masureel, M. / Janetzko, J. / Kobilka, B.K. / 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, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jun 17, 2020Group: Structure summary / Category: audit_author

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Assembly

Deposited unit
C: ARG-ARG-PRO-TYR-ILE-LEU
B: Beta-arrestin-1
R: Neurotensin receptor type 1
V: unidentified peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7735
Polymers78,0264
Non-polymers7471
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ARG-ARG-PRO-TYR-ILE-LEU


Mass: 819.007 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30990*PLUS
#2: Protein Beta-arrestin-1 / Arrestin / Arrestin beta-1 / Non-visual arrestin-2


Mass: 39062.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARRB1, ARR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P49407
#3: Protein Neurotensin receptor type 1 / NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH


Mass: 37360.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: missing regions were not modeled due to local low resolution/flexibility.
Source: (gene. exp.) Homo sapiens (human) / Gene: NTSR1, NTRR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30989
#4: Protein/peptide unidentified peptide


Mass: 783.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: actual sequence for this poly-A exists, however, the local resolution for this region is not sufficient to register the amino acids.
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#5: Chemical 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 / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: NTSR_Arrestin / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254725 / Symmetry type: POINT

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