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

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Entry
Database: EMDB / ID: 9382
TitleA high-resolution cryo-electron microscopy structure of a calcitonin receptor-heterotrimeric Gs protein complex
Map dataCalcitonin receptor-heterotrimeric Gs protein complex, Sharpened map (B -80)
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 / homologyActivation of the phototransduction cascade / Adrenaline,noradrenaline inhibits insulin secretion / G beta:gamma signalling through PI3Kgamma / GPCR, family 2, secretin-like, conserved site / Prostacyclin signalling through prostacyclin receptor / WD40-repeat-containing domain / Calcitonin, conserved site / WD40 repeat, conserved site / G-protein beta WD-40 repeat / Guanine nucleotide-binding protein, beta subunit ...Activation of the phototransduction cascade / Adrenaline,noradrenaline inhibits insulin secretion / G beta:gamma signalling through PI3Kgamma / GPCR, family 2, secretin-like, conserved site / Prostacyclin signalling through prostacyclin receptor / WD40-repeat-containing domain / Calcitonin, conserved site / WD40 repeat, conserved site / G-protein beta WD-40 repeat / Guanine nucleotide-binding protein, beta subunit / Ca2+ pathway / Calcitonin/adrenomedullin / Calcitonin-like / Calcitonin / P-loop containing nucleoside triphosphate hydrolase / G-protein gamma-like domain superfamily / GPCR, family 2-like / WD40/YVTN repeat-like-containing domain superfamily / G beta:gamma signalling through PLC beta / Inactivation, recovery and regulation of the phototransduction cascade / GPCR, family 2, secretin-like / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein, beta subunit / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / WD40 repeat / Olfactory Signaling Pathway / GPCR, family 2, calcitonin receptor / G-protein gamma-like domain / Calcitonin peptide-like / ADP signalling through P2Y purinoceptor 12 / G-protein, gamma subunit / GPCR, family 2, extracellular hormone receptor domain / GPCR, family 2, calcitonin receptor family / G protein alpha subunit, helical insertion / G alpha (q) signalling events / G alpha (12/13) signalling events / WD40-repeat-containing domain superfamily / Presynaptic function of Kainate receptors / Trp-Asp (WD) repeats profile. / Thromboxane signalling through TP receptor / Vasopressin regulates renal water homeostasis via Aquaporins / G-protein coupled receptors family 2 profile 1. / Thrombin signalling through proteinase activated receptors (PARs) / G-protein coupled receptors family 2 profile 2. / Trp-Asp (WD) repeats circular profile. / Calcitonin-like ligand receptors / Hedgehog 'off' state / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Glucagon signaling in metabolic regulation / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / PKA activation in glucagon signalling / G-protein activation / Glucagon-type ligand receptors / G alpha (z) signalling events / G-protein alpha subunit, group S / GPCR family 2, extracellular hormone receptor domain superfamily / Trp-Asp (WD) repeats signature. / G-protein coupled receptors family 2 signature 2. / G-protein coupled receptors family 2 signature 1. / Calcitonin / CGRP / IAPP family signature. / Hormone receptor domain / GGL domain / G-protein alpha subunit / G-protein gamma subunit domain profile. / WD domain, G-beta repeat / G alpha (s) signalling events / G alpha (i) signalling events / ADP signalling through P2Y purinoceptor 1 / Calcitonin / CGRP / IAPP family / 7 transmembrane receptor (Secretin family) / amylin receptor complex 3 / calcitonin binding / cross-receptor inhibition within G protein-coupled receptor heterodimer / amylin receptor complex 2 / amylin receptor activity / amylin receptor complex 1 / calcitonin receptor activity / calcitonin gene-related peptide receptor activity / positive regulation of calcium ion import across plasma membrane / amylin receptor signaling pathway / intracellular transport / positive regulation of adenylate cyclase activity / hair follicle placode formation / intrinsic component of membrane / cellular response to catecholamine stimulus / cardiac muscle cell apoptotic process / G protein-coupled acetylcholine receptor signaling pathway / adenylate cyclase-activating adrenergic receptor signaling pathway / sensory perception of taste / protein heterotrimerization / alkylglycerophosphoethanolamine phosphodiesterase activity / G-protein beta-subunit binding / adenylate cyclase-activating dopamine receptor signaling pathway / rhodopsin mediated signaling pathway / photoreceptor outer segment membrane / sensory perception of smell / bone development / developmental growth / G-protein beta/gamma-subunit complex binding
Function and homology information
SourceHomo sapiens (human) / Lama glama (llama) / Oncorhynchus sp. (fish)
Methodsingle particle reconstruction / cryo EM / 3.34 Å resolution
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
CitationJournal: to be published
Title: The molecular control of calcitonin receptor (CTR) 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
DateDeposition: Jan 2, 2019 / Header (metadata) release: Jan 23, 2019 / Map release: Jan 23, 2019 / Last update: Jan 23, 2019

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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
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6niy
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9382.map.gz (map file in CCP4 format, 23329 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
1.06 Å/pix.
= 190.8 Å
180 pix
1.06 Å/pix.
= 190.8 Å
180 pix
1.06 Å/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 Level:0.015 (by author), 0.015 (movie #1):
Minimum - Maximum-0.049256623 - 0.091105305
Average (Standard dev.)0.00024497448 (0.0029341842)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin0.00.00.0
Limit179.0179.0179.0
Spacing180180180
CellA=B=C: 190.79999 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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Mask #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: 5 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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