[English] 日本語
Yorodumi
- EMDB-20505: A complex structure of arrestin-2 bound to neurotensin receptor 1 -

+
Open data


ID or keywords:

Loading...

-
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 peptide
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Fab30 heavy chain
    • Protein or peptide: Fab30 light chain
Keywordscryo-EM structure / beta-arrestin / neurotensin receptor / beta-arrestin-GPCR complex / SIGNALING PROTEIN
Function / homology
Function and homology information


G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / positive regulation of locomotion / regulation of inositol trisphosphate biosynthetic process / angiotensin receptor binding / positive regulation of gamma-aminobutyric acid secretion / D-aspartate import across plasma membrane / TGFBR3 regulates TGF-beta signaling / Activation of SMO ...G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / positive regulation of locomotion / regulation of inositol trisphosphate biosynthetic process / angiotensin receptor binding / positive regulation of gamma-aminobutyric acid secretion / D-aspartate import across plasma membrane / TGFBR3 regulates TGF-beta signaling / Activation of SMO / positive regulation of arachidonate secretion / negative regulation of interleukin-8 production / L-glutamate import across plasma membrane / vocalization behavior / desensitization of G protein-coupled receptor signaling pathway / regulation of behavioral fear response / regulation of respiratory gaseous exchange / cAMP biosynthetic process / positive regulation of inhibitory postsynaptic potential / 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 / sensory perception / positive regulation of glutamate secretion / : / Lysosome Vesicle Biogenesis / response to food / regulation of membrane depolarization / response to lipid / stress fiber assembly / positive regulation of cardiac muscle hypertrophy / Golgi Associated Vesicle Biogenesis / positive regulation of inositol phosphate biosynthetic process / temperature homeostasis / positive regulation of Rho protein signal transduction / detection of temperature stimulus involved in sensory perception of pain / pseudopodium / negative regulation of interleukin-6 production / response to stress / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / conditioned place preference / insulin-like growth factor receptor binding / clathrin-coated pit / negative regulation of protein ubiquitination / enzyme inhibitor activity / intracellular glucose homeostasis / cytoplasmic vesicle membrane / Peptide ligand-binding receptors / Activated NOTCH1 Transmits Signal to the Nucleus / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / GTPase activator activity / adult locomotory behavior / neuropeptide signaling pathway / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein phosphorylation / G protein-coupled receptor binding / G protein-coupled receptor activity / cytoplasmic side of plasma membrane / 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 / Clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / cytoplasmic vesicle / G alpha (s) signalling events / molecular adaptor activity / G alpha (q) signalling events / dendritic spine / ubiquitin-dependent protein catabolic process / chemical synaptic transmission / proteasome-mediated ubiquitin-dependent protein catabolic process / perikaryon / positive regulation of ERK1 and ERK2 cascade / transcription coactivator activity / cell surface receptor signaling pathway / Ub-specific processing proteases / nuclear body / protein ubiquitination / positive regulation of apoptotic process / membrane raft / G protein-coupled receptor signaling pathway / Golgi membrane / lysosomal membrane / 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
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. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 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
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-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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

emd_20505.png

Downloads & links

-
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

Histogram

Histogram (log scale)
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

-
Supplemental data

-
Sample components

-
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 peptide
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Fab30 heavy chain
    • Protein or peptide: Fab30 light chain

-
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)

-
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

UniProtKB: Neurotensin receptor type 1

-
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

-
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

UniProtKB: Beta-arrestin-1

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

+
Image processing

CTF correctionSoftware - Name: Gctf / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4grv

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
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more