[English] 日本語
Yorodumi
- EMDB-20181: human Neurotensin Receptor 1 (hNTSR1) - Gi1 Protein Complex in no... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: EMD-20181
Titlehuman Neurotensin Receptor 1 (hNTSR1) - Gi1 Protein Complex in non-canonical conformation (NC state)
Map data
SamplehNTSR1-Gi1 complex in non-canonical conformation (NC state)
  • Neurotensin receptor type 1
  • JMV449
  • (Guanine nucleotide-binding protein ...) x 3
Function / homology
Function and homology information


G alpha (z) signalling events / Presynaptic function of Kainate receptors / Thrombin signalling through proteinase activated receptors (PARs) / Vasopressin regulates renal water homeostasis via Aquaporins / Thromboxane signalling through TP receptor / G beta:gamma signalling through PI3Kgamma / G alpha (i) signalling events / ADP signalling through P2Y purinoceptor 1 / Regulation of insulin secretion / G alpha (s) signalling events ...G alpha (z) signalling events / Presynaptic function of Kainate receptors / Thrombin signalling through proteinase activated receptors (PARs) / Vasopressin regulates renal water homeostasis via Aquaporins / Thromboxane signalling through TP receptor / G beta:gamma signalling through PI3Kgamma / G alpha (i) signalling events / ADP signalling through P2Y purinoceptor 1 / Regulation of insulin secretion / G alpha (s) signalling events / G beta:gamma signalling through PLC beta / G alpha (12/13) signalling events / G alpha (q) signalling events / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / Extra-nuclear estrogen signaling / G beta:gamma signalling through CDC42 / Adrenaline,noradrenaline inhibits insulin secretion / Prostacyclin signalling through prostacyclin receptor / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Olfactory Signaling Pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Peptide ligand-binding receptors / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / G-protein activation / Adenylate cyclase inhibitory pathway / Glucagon-type ligand receptors / Glucagon signaling in metabolic regulation / Activation of G protein gated Potassium channels / PLC beta mediated events / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / 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 / symmetric synapse / regulation of respiratory gaseous exchange / negative regulation of systemic arterial blood pressure / regulation of cAMP-mediated signaling / cardiac muscle cell apoptotic process / G protein-coupled serotonin receptor binding / G-protein beta/gamma-subunit complex / positive regulation of inositol phosphate biosynthetic process / sensory perception of taste / cellular response to catecholamine stimulus / positive regulation of protein localization to cell cortex / temperature homeostasis / G protein-coupled acetylcholine receptor signaling pathway / negative regulation of release of sequestered calcium ion into cytosol / alkylglycerophosphoethanolamine phosphodiesterase activity / protein heterotrimerization / positive regulation of arachidonic acid secretion / rhodopsin mediated signaling pathway / positive regulation of glutamate secretion / adenylate cyclase-activating dopamine receptor signaling pathway / cell cortex region / detection of temperature stimulus involved in sensory perception of pain / photoreceptor outer segment membrane / G-protein beta-subunit binding / positive regulation of cation channel activity / neuropeptide signaling pathway / photoreceptor disc membrane / spectrin binding / regulation of mitotic spindle organization / G-protein beta/gamma-subunit complex binding / negative regulation of synaptic transmission / cellular response to forskolin / heterotrimeric G-protein complex / Wnt signaling pathway, calcium modulating pathway / GTPase activating protein binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / extracellular vesicle / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cellular response to prostaglandin E stimulus / response to lipid / phospholipase C-activating G protein-coupled receptor signaling pathway / retina development in camera-type eye / cytoplasmic side of plasma membrane / adult locomotory behavior / GTPase binding / regulation of sensory perception of pain / photoreceptor inner segment / G protein-coupled receptor binding / response to peptide hormone / learning / dendritic shaft / positive regulation of release of sequestered calcium ion into cytosol / regulation of membrane depolarization / GDP binding / terminal bouton / cell body / midbody / lysosomal membrane / chemical synaptic transmission
WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / G-protein gamma subunit domain profile. / Trp-Asp (WD) repeats signature. / G-protein coupled receptors family 1 signature. / GGL domain / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit, group I / G-protein, beta subunit / WD40 repeat ...WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / G-protein gamma subunit domain profile. / Trp-Asp (WD) repeats signature. / G-protein coupled receptors family 1 signature. / GGL domain / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit, group I / G-protein, beta subunit / WD40 repeat / G-protein, gamma subunit / G-protein alpha subunit / 7 transmembrane receptor (rhodopsin family) / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / G-protein gamma-like domain superfamily / Neurotensin receptor / P-loop containing nucleoside triphosphate hydrolase / G-protein beta WD-40 repeat / Neurotensin type 1 receptor / G protein alpha subunit, helical insertion / WD40 repeat, conserved site / WD40-repeat-containing domain / GPCR, rhodopsin-like, 7TM / Guanine nucleotide-binding protein, beta subunit / G-protein coupled receptors family 1 profile. / G-alpha domain profile. / G-protein gamma-like domain / G protein-coupled receptor, rhodopsin-like / WD40/YVTN repeat-like-containing domain superfamily
Neurotensin receptor type 1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsKato HE / Zhang Y / Kobilka BK / Skiniotis G
CitationJournal: Nature / Year: 2019
Title: Conformational transitions of a neurotensin receptor 1-G complex.
Authors: Hideaki E Kato / Yan Zhang / Hongli Hu / Carl-Mikael Suomivuori / Francois Marie Ngako Kadji / Junken Aoki / Kaavya Krishna Kumar / Rasmus Fonseca / Daniel Hilger / Weijiao Huang / Naomi R Latorraca / Asuka Inoue / Ron O Dror / Brian K Kobilka / Georgios Skiniotis /
Abstract: Neurotensin receptor 1 (NTSR1) is a G-protein-coupled receptor (GPCR) that engages multiple subtypes of G protein, and is involved in the regulation of blood pressure, body temperature, weight and ...Neurotensin receptor 1 (NTSR1) is a G-protein-coupled receptor (GPCR) that engages multiple subtypes of G protein, and is involved in the regulation of blood pressure, body temperature, weight and the response to pain. Here we present structures of human NTSR1 in complex with the agonist JMV449 and the heterotrimeric G protein, at a resolution of 3 Å. We identify two conformations: a canonical-state complex that is similar to recently reported GPCR-G complexes (in which the nucleotide-binding pocket adopts more flexible conformations that may facilitate nucleotide exchange), and a non-canonical state in which the G protein is rotated by about 45 degrees relative to the receptor and exhibits a more rigid nucleotide-binding pocket. In the non-canonical state, NTSR1 exhibits features of both active and inactive conformations, which suggests that the structure may represent an intermediate form along the activation pathway of G proteins. This structural information, complemented by molecular dynamics simulations and functional studies, provides insights into the complex process of G-protein activation.
Validation ReportPDB-ID: 6osa

SummaryFull reportAbout validation report
DateDeposition: May 1, 2019 / Header (metadata) release: Jul 10, 2019 / Map release: Jul 10, 2019 / Update: Jul 10, 2019

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6osa
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_20181.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å
1.06 Å/pix.
x 240 pix.
= 254.4 Å
1.06 Å/pix.
x 240 pix.
= 254.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.24982679 - 0.41312334
Average (Standard dev.)-0.0003549454 (±0.010895068)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z254.400254.400254.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.2500.413-0.000

-
Supplemental data

-
Sample components

+
Entire hNTSR1-Gi1 complex in non-canonical conformation (NC state)

EntireName: hNTSR1-Gi1 complex in non-canonical conformation (NC state)
Number of components: 6

+
Component #1: protein, hNTSR1-Gi1 complex in non-canonical conformation (NC state)

ProteinName: hNTSR1-Gi1 complex in non-canonical conformation (NC state)
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

+
Component #2: protein, Neurotensin receptor type 1

ProteinName: Neurotensin receptor type 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.396734 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

+
Component #3: protein, JMV449

ProteinName: JMV449 / Details: JMV449 from Tocris Bioscience. / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.762979 kDa
SourceSpecies: synthetic construct (others)

+
Component #4: protein, Guanine nucleotide-binding protein G(i) subunit alpha-1

ProteinName: Guanine nucleotide-binding protein G(i) subunit alpha-1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.415031 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #5: protein, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subuni...

ProteinName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.671102 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #6: protein, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subuni...

ProteinName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.861143 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 75 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 207119
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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