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- EMDB-20181: human Neurotensin Receptor 1 (hNTSR1) - Gi1 Protein Complex in no... -

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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


inositol phosphate catabolic process / G protein-coupled neurotensin receptor activity / regulation of action potential / L-glutamate import across plasma membrane / positive regulation of inhibitory postsynaptic potential / D-aspartate import across plasma membrane / symmetric synapse / positive regulation of gamma-aminobutyric acid secretion / negative regulation of systemic arterial blood pressure / G protein-coupled serotonin receptor binding ...inositol phosphate catabolic process / G protein-coupled neurotensin receptor activity / regulation of action potential / L-glutamate import across plasma membrane / positive regulation of inhibitory postsynaptic potential / D-aspartate import across plasma membrane / symmetric synapse / positive regulation of gamma-aminobutyric acid secretion / negative regulation of systemic arterial blood pressure / G protein-coupled serotonin receptor binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / negative regulation of release of sequestered calcium ion into cytosol / positive regulation of arachidonic acid secretion / positive regulation of inositol phosphate biosynthetic process / temperature homeostasis / cardiac muscle cell apoptotic process / sensory perception of taste / regulation of respiratory gaseous exchange / G-protein beta/gamma-subunit complex / cellular response to catecholamine stimulus / positive regulation of glutamate secretion / G protein-coupled acetylcholine receptor signaling pathway / detection of temperature stimulus involved in sensory perception of pain / positive regulation of cation channel activity / alkylglycerophosphoethanolamine phosphodiesterase activity / cell cortex region / rhodopsin mediated signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / G-protein beta-subunit binding / photoreceptor outer segment membrane / regulation of mitotic spindle organization / neuropeptide signaling pathway / photoreceptor disc membrane / cellular response to forskolin / spectrin binding / negative regulation of synaptic transmission / G-protein beta/gamma-subunit complex binding / heterotrimeric G-protein complex / GTPase activating protein binding / G protein-coupled receptor activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / extracellular vesicle / Wnt signaling pathway, calcium modulating pathway / cellular response to prostaglandin E stimulus / cytoplasmic side of plasma membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of sensory perception of pain / retina development in camera-type eye / adult locomotory behavior / GTPase binding / response to peptide hormone / G protein-coupled receptor binding / dendritic shaft / photoreceptor inner segment / response to lipid / positive regulation of release of sequestered calcium ion into cytosol / learning / GDP binding / terminal bouton / regulation of membrane depolarization / cell population proliferation / cell body / midbody / lysosomal membrane / cellular response to hypoxia / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / platelet activation / Ras protein signal transduction / protein N-terminus binding / protein folding / perikaryon / dendritic spine / cell cycle / GTPase activity / cell division / centrosome / synapse / G protein-coupled receptor signaling pathway / positive regulation of apoptotic process / membrane raft / GTP binding / dendrite / protein-containing complex binding / signal transduction / negative regulation of apoptotic process / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / cell surface / integral component of plasma membrane / mitochondrion / go:0005623: / extracellular exosome / membrane / identical protein binding / plasma membrane / nucleus
G-protein, gamma subunit / G-protein beta WD-40 repeat / G-protein gamma-like domain / Neurotensin receptor / G protein alpha subunit, helical insertion / Neurotensin type 1 receptor / Guanine nucleotide-binding protein, beta subunit / GPCR, rhodopsin-like, 7TM / WD40-repeat-containing domain / WD40/YVTN repeat-like-containing domain superfamily ...G-protein, gamma subunit / G-protein beta WD-40 repeat / G-protein gamma-like domain / Neurotensin receptor / G protein alpha subunit, helical insertion / Neurotensin type 1 receptor / Guanine nucleotide-binding protein, beta subunit / GPCR, rhodopsin-like, 7TM / WD40-repeat-containing domain / WD40/YVTN repeat-like-containing domain superfamily / WD40 repeat, conserved site / P-loop containing nucleoside triphosphate hydrolase / G-protein gamma-like domain superfamily / WD40 repeat / G-protein, beta subunit / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein-coupled receptor, rhodopsin-like / WD40-repeat-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
Funding support Japan, United States, Denmark, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H03163 Japan
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM127359 United States
Novo Nordisk FoundationNNF15OC0015268 Denmark
Japan Agency for Medical Research and Development (AMED)JP17gm0010004 Japan
Japan Agency for Medical Research and Development (AMED)JP17gm5910013 Japan
Japan Society for the Promotion of Science (JSPS)17K08264 Japan
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 ...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
History
DepositionMay 1, 2019-
Header (metadata) releaseJul 10, 2019-
Map releaseJul 10, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

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

Downloads & links

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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

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Supplemental data

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Sample components

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

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

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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)

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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)

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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)

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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)

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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)

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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)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
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: 75 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

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

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Atomic model buiding

Output model

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