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- EMDB-20505: A complex structure of arrestin-2 bound to neurotensin receptor 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-20505
TitleA complex structure of arrestin-2 bound to neurotensin receptor 1
Map data
Sample
  • Complex: Fusion complex of Bril-NTSR1-beta-arrestin1-fab30
    • Protein or peptide: Neurotensin receptor type 1
    • Protein or peptide: Neurotensin peptideNeurotensin
    • Protein or peptide: Beta-arrestin-1Arrestin
    • Protein or peptide: Fab30 heavy chain
    • Protein or peptide: Fab30 light chain
Function / homology
Function and homology information


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 ...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 / 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 / clathrin-coated pit / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / visual perception / Activated NOTCH1 Transmits Signal to the Nucleus / 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 / ubiquitin-dependent protein catabolic process / chemical synaptic transmission / perikaryon / cytoplasmic vesicle / G alpha (s) signalling events / G alpha (q) signalling events / proteasome-mediated ubiquitin-dependent protein catabolic process / dendritic spine / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / 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 / 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 / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Beta-arrestin-1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsYin W / Li Z / Jin M / Yin Y-L / de Waal PW / Pal K / Gao X / He Y / Gao J / Wang X ...Yin W / Li Z / Jin M / Yin Y-L / de Waal PW / Pal K / Gao X / He Y / Gao J / Wang X / Zhang Y / Zhou H / Melcher K / Jiang Y / Cong Y / Zhou XE / Yu X / Xu HE
Funding support United States, China, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127710 United States
Ministry of Science and Technology (MoST, China)XDB08020303 China
CitationJournal: Cell Res / Year: 2019
Title: A complex structure of arrestin-2 bound to a G protein-coupled receptor.
Authors: Wanchao Yin / Zhihai Li / Mingliang Jin / Yu-Ling Yin / Parker W de Waal / Kuntal Pal / Yanting Yin / Xiang Gao / Yuanzheng He / Jing Gao / Xiaoxi Wang / Yan Zhang / Hu Zhou / Karsten ...Authors: Wanchao Yin / Zhihai Li / Mingliang Jin / Yu-Ling Yin / Parker W de Waal / Kuntal Pal / Yanting Yin / Xiang Gao / Yuanzheng He / Jing Gao / Xiaoxi Wang / Yan Zhang / Hu Zhou / Karsten Melcher / Yi Jiang / Yao Cong / X Edward Zhou / Xuekui Yu / H Eric Xu /
Abstract: Arrestins comprise a family of signal regulators of G-protein-coupled receptors (GPCRs), which include arrestins 1 to 4. While arrestins 1 and 4 are visual arrestins dedicated to rhodopsin, arrestins ...Arrestins comprise a family of signal regulators of G-protein-coupled receptors (GPCRs), which include arrestins 1 to 4. While arrestins 1 and 4 are visual arrestins dedicated to rhodopsin, arrestins 2 and 3 (Arr2 and Arr3) are β-arrestins known to regulate many nonvisual GPCRs. The dynamic and promiscuous coupling of Arr2 to nonvisual GPCRs has posed technical challenges to tackle the basis of arrestin binding to GPCRs. Here we report the structure of Arr2 in complex with neurotensin receptor 1 (NTSR1), which reveals an overall assembly that is strikingly different from the visual arrestin-rhodopsin complex by a 90° rotation of Arr2 relative to the receptor. In this new configuration, intracellular loop 3 (ICL3) and transmembrane helix 6 (TM6) of the receptor are oriented toward the N-terminal domain of the arrestin, making it possible for GPCRs that lack the C-terminal tail to couple Arr2 through their ICL3. Molecular dynamics simulation and crosslinking data further support the assembly of the Arr2‒NTSR1 complex. Sequence analysis and homology modeling suggest that the Arr2‒NTSR1 complex structure may provide an alternative template for modeling arrestin-GPCR interactions.
History
DepositionJul 22, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseDec 4, 2019-
UpdateJan 8, 2020-
Current statusJan 8, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pwc
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6pwc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20505.png

Downloads & links

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Map

FileDownload / File: emd_20505.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.031 Å
Density
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.02117386 - 0.045307215
Average (Standard dev.)-0.0002145957 (±0.0025143754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.936 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0311.0311.031
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z263.936263.936263.936
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0210.045-0.000

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Supplemental data

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Sample components

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Entire : Fusion complex of Bril-NTSR1-beta-arrestin1-fab30

EntireName: Fusion complex of Bril-NTSR1-beta-arrestin1-fab30
Components
  • Complex: Fusion complex of Bril-NTSR1-beta-arrestin1-fab30
    • Protein or peptide: Neurotensin receptor type 1
    • Protein or peptide: Neurotensin peptideNeurotensin
    • Protein or peptide: Beta-arrestin-1Arrestin
    • Protein or peptide: Fab30 heavy chain
    • Protein or peptide: Fab30 light chain

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Supramolecule #1: Fusion complex of Bril-NTSR1-beta-arrestin1-fab30

SupramoleculeName: Fusion complex of Bril-NTSR1-beta-arrestin1-fab30 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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: 41.555387 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: APSSELDVNT DIYSKVLVTA VYLALFVVGT VGNTVTAFTL ARKKSLQSLQ STVHYHLGSL ALSDLLTLLL AMPVELYNFI WVHHPWAFG DAGCRGYYFL RDACTYATAL NVASLSVERY LAICHPFKAK TLMSRSRTKK FISAIWLASA LLAVPMLFTM G EQNRSADG ...String:
APSSELDVNT DIYSKVLVTA VYLALFVVGT VGNTVTAFTL ARKKSLQSLQ STVHYHLGSL ALSDLLTLLL AMPVELYNFI WVHHPWAFG DAGCRGYYFL RDACTYATAL NVASLSVERY LAICHPFKAK TLMSRSRTKK FISAIWLASA LLAVPMLFTM G EQNRSADG QHAGGLVCTP TIHTATVKVV IQVNTFMSFI FPMVVISVLN TIIANKLTVM VRQAAEQGQV CTVGGEHSTF SM AIEPGRV QALRHGVRVL RAVVIAFVVC WLPYHVRRLM FCYISDEQWT PFLYDFYHYF YMVTNALFYV SSTINPILYN LVS ANFRHI FLATLACLCP VWRRRRKRPA FSRKADSVSS NHTLSSNATR ETLY

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Macromolecule #2: Neurotensin peptide

MacromoleculeName: Neurotensin peptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 819.007 Da
SequenceString:
RRPYIL

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Macromolecule #3: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.161359 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF CANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF CANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI RKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD ICLFNTA QYKCPVAMEE ADDTVAPSST FCKVYTLTPF LCNNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSDVAVE LPFTLMHPKP KEEPPHREVP ENETPVDTNL IELDTNDDDA AAEDFAR

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Macromolecule #4: Fab30 heavy chain

MacromoleculeName: Fab30 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.689643 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEISEVQLVE SGGGLVQPGG SLRLSCAASG FNVYSSSIHW VRQAPGKGLE WVASISSYYC YTYYADSVKG RFTISADTSK NTAYLQMNS LRAEDTAVYY CARSRQFWYS GLDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
MEISEVQLVE SGGGLVQPGG SLRLSCAASG FNVYSSSIHW VRQAPGKGLE WVASISSYYC YTYYADSVKG RFTISADTSK NTAYLQMNS LRAEDTAVYY CARSRQFWYS GLDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD KTHHHHHHHH

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Macromolecule #5: Fab30 light chain

MacromoleculeName: Fab30 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.435064 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 68.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4grv

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 260322

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