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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
SampleFusion complex of Bril-NTSR1-beta-arrestin1-fab30:
Neurotensin receptor type 1 / Neurotensin peptideNeurotensin / Beta-arrestin-1Arrestin / Fab30 heavy chain / Fab30 light chain
Function / homology
Function and homology information


V2 vasopressin receptor binding / follicle-stimulating hormone receptor binding / alpha-1A adrenergic receptor binding / angiotensin receptor binding / inositol phosphate catabolic process / G protein-coupled neurotensin receptor activity / follicle-stimulating hormone signaling pathway / alpha-1B adrenergic receptor binding / L-glutamate import across plasma membrane / positive regulation of inhibitory postsynaptic potential ...V2 vasopressin receptor binding / follicle-stimulating hormone receptor binding / alpha-1A adrenergic receptor binding / angiotensin receptor binding / inositol phosphate catabolic process / G protein-coupled neurotensin receptor activity / follicle-stimulating hormone signaling pathway / alpha-1B adrenergic receptor binding / L-glutamate import across plasma membrane / positive regulation of inhibitory postsynaptic potential / D-aspartate import across plasma membrane / symmetric synapse / regulation of action potential / AP-2 adaptor complex binding / protein phosphorylated amino acid binding / positive regulation of histone H4 acetylation / positive regulation of smooth muscle cell apoptotic process / positive regulation of gamma-aminobutyric acid secretion / negative regulation of systemic arterial blood pressure / negative regulation of interleukin-8 production / G protein-coupled receptor internalization / clathrin adaptor activity / negative regulation of release of sequestered calcium ion into cytosol / positive regulation of arachidonic acid secretion / arrestin family protein binding / positive regulation of inositol phosphate biosynthetic process / temperature homeostasis / regulation of respiratory gaseous exchange / positive regulation of cation channel activity / detection of temperature stimulus involved in sensory perception of pain / positive regulation of glutamate secretion / stress fiber assembly / enzyme inhibitor activity / positive regulation of Rho protein signal transduction / neuropeptide signaling pathway / mitogen-activated protein kinase kinase binding / negative regulation of GTPase activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of receptor internalization / pseudopodium / negative regulation of NF-kappaB transcription factor activity / response to lipid / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of Notch signaling pathway / phototransduction / G protein-coupled receptor activity / histone acetylation / cytoplasmic side of plasma membrane / negative regulation of interleukin-6 production / clathrin-coated pit / regulation of sensory perception of pain / negative regulation of protein ubiquitination / adult locomotory behavior / insulin-like growth factor receptor binding / G protein-coupled receptor binding / dendritic shaft / GTPase activator activity / positive regulation of histone acetylation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein ubiquitination / positive regulation of release of sequestered calcium ion into cytosol / negative regulation of ERK1 and ERK2 cascade / learning / chromatin / estrogen receptor binding / terminal bouton / regulation of membrane depolarization / protein transport / proteasome-mediated ubiquitin-dependent protein catabolic process / lysosomal membrane / chemical synaptic transmission / cytoplasmic vesicle membrane / postsynaptic membrane / membrane organization / platelet activation / protein N-terminus binding / ion channel binding / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / perikaryon / positive regulation of peptidyl-serine phosphorylation / basolateral plasma membrane / transcription coactivator activity / positive regulation of protein binding / nuclear body / negative regulation of neuron apoptotic process / activation of MAPK activity / dendritic spine / postsynaptic density / positive regulation of ERK1 and ERK2 cascade / endosome / protein ubiquitination / Golgi membrane / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / membrane raft / regulation of transcription by RNA polymerase II / positive regulation of apoptotic process / transcription factor binding / protein-containing complex binding
Arrestin / Arrestin-like, N-terminal / Neurotensin type 1 receptor / Neurotensin receptor / Arrestin, C-terminal / Arrestin, N-terminal / Immunoglobulin E-set / GPCR, rhodopsin-like, 7TM / G protein-coupled receptor, rhodopsin-like / Arrestin C-terminal-like domain / Arrestin, conserved site
Neurotensin receptor type 1 / Beta-arrestin-1
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.
Validation ReportPDB-ID: 6pwc

SummaryFull reportAbout validation report
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

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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 256 pix.
= 263.936 Å
1.03 Å/pix.
x 256 pix.
= 263.936 Å
1.03 Å/pix.
x 256 pix.
= 263.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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 / Number of components: 6

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Component #1: protein, Fusion complex of Bril-NTSR1-beta-arrestin1-fab30

ProteinName: Fusion complex of Bril-NTSR1-beta-arrestin1-fab30 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, Neurotensin receptor type 1

ProteinName: Neurotensin receptor type 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.555387 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, Neurotensin peptide

ProteinName: Neurotensin peptideNeurotensin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.819007 kDa
SourceSpecies: synthetic construct (others)

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Component #4: protein, Beta-arrestin-1

ProteinName: Beta-arrestin-1Arrestin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.161359 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #5: protein, Fab30 heavy chain

ProteinName: Fab30 heavy chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.689643 kDa
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #6: protein, Fab30 light chain

ProteinName: Fab30 light chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.435064 kDa
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 68 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 BASE (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 260322
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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