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- EMDB-9382: A high-resolution cryo-electron microscopy structure of a calcito... -

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Basic information

Entry
Database: EMDB / ID: EMD-9382
TitleA high-resolution cryo-electron microscopy structure of a calcitonin receptor-heterotrimeric Gs protein complex
Map data
SampleComplex of a full-length, active-state calcitonin receptor with peptide ligand, heterotrimeric Gs protein and nanobody 35
  • (Guanine nucleotide-binding protein ...) x 3
  • Nanobody35
  • Calcitonin receptor
  • Calcitonin
Function / homology
Function and homology information


calcitonin binding / cross-receptor inhibition within G protein-coupled receptor heterodimer / amylin receptor complex 3 / amylin receptor complex 2 / amylin receptor complex 1 / amylin receptor activity / calcitonin receptor activity / calcitonin gene-related peptide receptor activity / positive regulation of calcium ion import across plasma membrane / amylin receptor signaling pathway ...calcitonin binding / cross-receptor inhibition within G protein-coupled receptor heterodimer / amylin receptor complex 3 / amylin receptor complex 2 / amylin receptor complex 1 / amylin receptor activity / calcitonin receptor activity / calcitonin gene-related peptide receptor activity / positive regulation of calcium ion import across plasma membrane / amylin receptor signaling pathway / positive regulation of adenylate cyclase activity / intracellular transport / intrinsic component of membrane / hair follicle placode formation / cardiac muscle cell apoptotic process / sensory perception of taste / G-protein beta/gamma-subunit complex / cellular response to catecholamine stimulus / G protein-coupled acetylcholine receptor signaling pathway / adenylate cyclase-activating adrenergic receptor signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / positive regulation of cAMP-mediated signaling / bone development / rhodopsin mediated signaling pathway / sensory perception of smell / adenylate cyclase-activating dopamine receptor signaling pathway / G-protein beta-subunit binding / photoreceptor outer segment membrane / developmental growth / photoreceptor disc membrane / activation of adenylate cyclase activity / spectrin binding / G-protein beta/gamma-subunit complex binding / heterotrimeric G-protein complex / cellular response to glucagon stimulus / renal water homeostasis / positive regulation of protein kinase A signaling / adenylate cyclase activator activity / response to amyloid-beta / extracellular vesicle / Wnt signaling pathway, calcium modulating pathway / cellular response to prostaglandin E stimulus / trans-Golgi network membrane / adenylate cyclase-activating G protein-coupled receptor signaling pathway / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of insulin secretion / GTPase binding / photoreceptor inner segment / cognition / positive regulation of cell death / platelet aggregation / response to glucocorticoid / hormone activity / positive regulation of GTPase activity / positive regulation of cold-induced thermogenesis / cell body / lysosomal membrane / cellular response to hypoxia / positive regulation of cytosolic calcium ion concentration / platelet activation / amyloid-beta binding / Ras protein signal transduction / cell population proliferation / protein folding / positive regulation of peptidyl-serine phosphorylation / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / GTPase activity / positive regulation of protein kinase B signaling / synapse / protein-containing complex binding / G protein-coupled receptor signaling pathway / axon / GTP binding / dendrite / positive regulation of gene expression / signal transduction / integral component of plasma membrane / cell / extracellular exosome / membrane / extracellular region / plasma membrane / metal ion binding / cytosol / cytoplasm
G-protein alpha subunit, group S / Calcitonin, conserved site / G-protein, gamma subunit / GPCR, family 2, calcitonin receptor / GPCR, family 2, extracellular hormone receptor domain / GPCR, family 2, secretin-like / GPCR, family 2, calcitonin receptor family / G protein alpha subunit, helical insertion / G-protein gamma-like domain / WD40 repeat ...G-protein alpha subunit, group S / Calcitonin, conserved site / G-protein, gamma subunit / GPCR, family 2, calcitonin receptor / GPCR, family 2, extracellular hormone receptor domain / GPCR, family 2, secretin-like / GPCR, family 2, calcitonin receptor family / G protein alpha subunit, helical insertion / G-protein gamma-like domain / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / GPCR, family 2, secretin-like, conserved site / WD40-repeat-containing domain / GPCR, family 2-like / WD40 repeat, conserved site / Calcitonin-like / GPCR family 2, extracellular hormone receptor domain superfamily / WD40-repeat-containing domain superfamily / G-protein beta WD-40 repeat / G-protein gamma-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Calcitonin / Calcitonin peptide-like / Calcitonin/adrenomedullin
Calcitonin receptor / 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(s) subunit alpha isoforms short / Calcitonin
Biological speciesHomo sapiens (human) / Lama glama (llama) / Oncorhynchus sp. (fish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
Authorsdal Maso E / Glukhova A / Zhu Y / Garcia-Nafria J / Tate CG / Atanasio S / Reynolds CA / Ramirez-Aportela E / Carazo J-M / Hick CA / Furness SGB / Hay DL / Liang Y-L / Miller LJ / Christopoulos A / Wang M-W / Wootten D / Sexton PM
Funding support Australia, 4 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1061044 Australia
National Health and Medical Research Council (NHMRC, Australia)1055134 Australia
National Health and Medical Research Council (NHMRC, Australia)1065410 Australia
National Health and Medical Research Council (NHMRC, Australia)1126857 Australia
CitationJournal: Acs Pharmacol Transl Sci / Year: 2019
Title: The Molecular Control of Calcitonin Receptor Signaling
Authors: dal Maso E / Glukhova A / Zhu Y / Garcia-Nafria J / Tate CG / Atanasio S / Reynolds CA / Ramirez-Aportela E / Carazo J-M / Hick CA / Furness SGB / Hay DL / Liang Y-L / Miller LJ / Christopoulos A / Wang M-W / Wootten D / Sexton PM
Validation ReportPDB-ID: 6niy

SummaryFull reportAbout validation report
History
DepositionJan 2, 2019-
Header (metadata) releaseJan 23, 2019-
Map releaseJan 23, 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: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6niy
  • Surface level: 0.015
  • 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_9382.map.gz / Format: CCP4 / Size: 22.2 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 180 pix.
= 190.8 Å
1.06 Å/pix.
x 180 pix.
= 190.8 Å
1.06 Å/pix.
x 180 pix.
= 190.8 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: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.049256623 - 0.091105305
Average (Standard dev.)0.00024497448 (±0.0029341842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 190.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z190.800190.800190.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0490.0910.000

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Supplemental data

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Segmentation: #1

Fileemd_9382_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Complex of a full-length, active-state calcitonin receptor with p...

EntireName: Complex of a full-length, active-state calcitonin receptor with peptide ligand, heterotrimeric Gs protein and nanobody 35
Number of components: 7

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Component #1: protein, Complex of a full-length, active-state calcitonin recept...

ProteinName: Complex of a full-length, active-state calcitonin receptor with peptide ligand, heterotrimeric Gs protein and nanobody 35
Recombinant expression: No
MassTheoretical: 150 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #2: protein, Guanine nucleotide-binding protein G(s) subunit alpha is...

ProteinName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.72552 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: protein, Nanobody35

ProteinName: Nanobody35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.140742 kDa
SourceSpecies: Lama glama (llama)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Calcitonin receptor

ProteinName: Calcitonin receptor / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.387316 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: 37.41693 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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Component #7: protein, Calcitonin

ProteinName: Calcitonin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.438886 kDa
SourceSpecies: Oncorhynchus sp. (fish)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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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: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 47170.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 417949
3D reconstructionSoftware: RELION / CTF correction: Phase Plate CTF correction / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 5UZ7
Output model

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