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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 / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / inositol phosphate catabolic process / G protein-coupled neurotensin receptor activity / L-glutamate import across plasma membrane / regulation of action potential ...V2 vasopressin receptor binding / follicle-stimulating hormone receptor binding / alpha-1A adrenergic receptor binding / angiotensin receptor binding / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / inositol phosphate catabolic process / G protein-coupled neurotensin receptor activity / L-glutamate import across plasma membrane / regulation of action potential / positive regulation of gamma-aminobutyric acid secretion / positive regulation of inhibitory postsynaptic potential / D-aspartate import across plasma membrane / positive regulation of histone H4 acetylation / AP-2 adaptor complex binding / protein phosphorylated amino acid binding / symmetric synapse / negative regulation of interleukin-8 production / regulation of respiratory gaseous exchange / positive regulation of smooth muscle cell apoptotic process / clathrin adaptor activity / negative regulation of systemic arterial blood pressure / positive regulation of inositol phosphate biosynthetic process / negative regulation of release of sequestered calcium ion into cytosol / G protein-coupled receptor internalization / temperature homeostasis / arrestin family protein binding / positive regulation of arachidonic acid secretion / positive regulation of glutamate secretion / detection of temperature stimulus involved in sensory perception of pain / enzyme inhibitor activity / positive regulation of cation channel activity / neuropeptide signaling pathway / stress fiber assembly / positive regulation of Rho protein signal transduction / mitogen-activated protein kinase kinase binding / negative regulation of GTPase activity / positive regulation of receptor internalization / G protein-coupled receptor activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / pseudopodium / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of NF-kappaB transcription factor activity / positive regulation of histone acetylation / negative regulation of interleukin-6 production / negative regulation of Notch signaling pathway / phototransduction / response to lipid / histone acetylation / clathrin-coated pit / cytoplasmic side of plasma membrane / regulation of sensory perception of pain / adult locomotory behavior / negative regulation of protein ubiquitination / G protein-coupled receptor binding / insulin-like growth factor receptor binding / GTPase activator activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / dendritic shaft / positive regulation of protein ubiquitination / positive regulation of release of sequestered calcium ion into cytosol / learning / negative regulation of ERK1 and ERK2 cascade / chromatin / terminal bouton / cytoplasmic vesicle membrane / estrogen receptor binding / protein transport / regulation of membrane depolarization / lysosomal membrane / chemical synaptic transmission / proteasome-mediated ubiquitin-dependent protein catabolic process / platelet activation / membrane organization / protein N-terminus binding / transcription by RNA polymerase II / postsynaptic membrane / transcription regulatory region DNA binding / ion channel binding / positive regulation of peptidyl-serine phosphorylation / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / response to drug / basolateral plasma membrane / perikaryon / positive regulation of protein binding / nuclear body / activation of MAPK activity / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / dendritic spine / postsynaptic density / endosome / protein ubiquitination / positive regulation of protein phosphorylation / membrane raft / Golgi membrane / G protein-coupled receptor signaling pathway / positive regulation of apoptotic process / transcription factor binding
Neurotensin type 1 receptor / Arrestin-like, N-terminal / Neurotensin receptor / Arrestin / Arrestin, C-terminal / Arrestin, N-terminal / Immunoglobulin E-set / GPCR, rhodopsin-like, 7TM / Arrestin, conserved site / Arrestin C-terminal-like domain / G protein-coupled receptor, rhodopsin-like
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 / 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 SciencesR01GM127710 United States
Ministry of Science and Technology (China)XDB08020303 China
CitationJournal: To Be Published
Title: A complex structure of arrestin-2 bound to a G protein-coupled receptor
Authors: 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
Validation ReportPDB-ID: 6pwc

SummaryFull reportAbout validation report
History
DepositionJul 22, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseDec 4, 2019-
UpdateDec 4, 2019-
Current statusDec 4, 2019Processing 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
  • Download
  • 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 models: PDB-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
start NX/NY/NZ111-94150
NX/NY/NZ111123111
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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