[English] 日本語
Yorodumi- PDB-6pwc: A complex structure of arrestin-2 bound to neurotensin receptor 1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pwc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | A complex structure of arrestin-2 bound to neurotensin receptor 1 | |||||||||
Components |
| |||||||||
Keywords | SIGNALING PROTEIN / cryo-EM structure / beta-arrestin / neurotensin receptor / beta-arrestin-GPCR complex | |||||||||
Function / homology | Function and homology information G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / angiotensin receptor binding / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / Activation of SMO / response to lipid / negative regulation of interleukin-8 production / regulation of membrane depolarization ...G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / angiotensin receptor binding / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / Activation of SMO / response to lipid / negative regulation of interleukin-8 production / regulation of membrane depolarization / positive regulation of arachidonate secretion / L-glutamate import across plasma membrane / regulation of respiratory gaseous exchange / positive regulation of inhibitory postsynaptic potential / arrestin family protein binding / G protein-coupled receptor internalization / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of systemic arterial blood pressure / positive regulation of glutamate secretion / enzyme inhibitor activity / positive regulation of inositol phosphate biosynthetic process / Lysosome Vesicle Biogenesis / positive regulation of Rho protein signal transduction / negative regulation of NF-kappaB transcription factor activity / temperature homeostasis / Golgi Associated Vesicle Biogenesis / negative regulation of Notch signaling pathway / stress fiber assembly / 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 / learning / dendritic shaft / 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 / Cargo recognition for clathrin-mediated endocytosis / Signaling by BRAF and RAF1 fusions / Clathrin-mediated endocytosis / protein transport / Thrombin signalling through proteinase activated receptors (PARs) / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / G alpha (s) signalling events / G alpha (q) signalling events / chemical synaptic transmission / perikaryon / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / dendritic spine / nuclear body / Ub-specific processing proteases / protein ubiquitination / positive regulation of protein phosphorylation / membrane raft / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / lysosomal membrane / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / positive regulation of gene expression / chromatin / negative regulation of apoptotic process / protein-containing complex binding / cell surface / Golgi apparatus / signal transduction / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Yin, W. / Li, Z. / Jin, M. / Yin, Y.-L. / de Waal, P.W. / Pal, K. / Gao, X. / He, Y. / Gao, J. / Wang, X. ...Yin, W. / Li, Z. / Jin, M. / Yin, Y.-L. / de Waal, P.W. / Pal, K. / Gao, X. / He, Y. / Gao, J. / Wang, X. / Zhang, Y. / Zhou, H. / Melcher, K. / Jiang, Y. / Cong, Y. / Zhou, X.E. / Yu, X. / Xu, H.E. | |||||||||
Funding support | United States, China, 2items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6pwc.cif.gz | 166.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6pwc.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 6pwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pwc_validation.pdf.gz | 763.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6pwc_full_validation.pdf.gz | 764.8 KB | Display | |
Data in XML | 6pwc_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 6pwc_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/6pwc ftp://data.pdbj.org/pub/pdb/validation_reports/pw/6pwc | HTTPS FTP |
-Related structure data
Related structure data | 20505MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 41555.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NTSR1, NTRR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30989 |
---|---|
#2: Protein/peptide | Mass: 819.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Protein | Mass: 44161.359 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 |
#4: Antibody | Mass: 25689.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Spodoptera frugiperda (fall armyworm) |
#5: Antibody | Mass: 23435.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Spodoptera frugiperda (fall armyworm) |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Fusion complex of Bril-NTSR1-beta-arrestin1-fab30 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 68 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement |
---|---|
EM software | Name: Gctf / Category: CTF correction |
CTF correction | Type: NONE |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260322 / Symmetry type: POINT |