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- EMDB-8978: Cryo-EM structure of the active, Gs-protein complexed, human CGRP... -

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Entry
Database: EMDB / ID: 8978
TitleCryo-EM structure of the active, Gs-protein complexed, human CGRP receptor
Map dataActive, Gs-protein complexed, CGRP receptor
SampleComplex of a full-length, active-state calcitonin gene-related peptide receptor with calcitonin gene-related peptide ligand, heterotrimeric Gs protein and nanobody35
  • (Calcitonin gene-related peptide ...) x 2
  • Nanobody 35Single-domain antibody
  • (Guanine nucleotide-binding protein ...) x 3
  • Receptor activity-modifying protein 1
Function / homologyActivation of G protein gated Potassium channels / GPCR, family 2-like / Calcitonin gene-related peptide / G-protein gamma-like domain / WD40/YVTN repeat-like-containing domain superfamily / Adrenaline,noradrenaline inhibits insulin secretion / Guanine nucleotide-binding protein, beta subunit / Ca2+ pathway / GPCR, family 2, secretin-like, conserved site / Prostacyclin signalling through prostacyclin receptor ...Activation of G protein gated Potassium channels / GPCR, family 2-like / Calcitonin gene-related peptide / G-protein gamma-like domain / WD40/YVTN repeat-like-containing domain superfamily / Adrenaline,noradrenaline inhibits insulin secretion / Guanine nucleotide-binding protein, beta subunit / Ca2+ pathway / GPCR, family 2, secretin-like, conserved site / Prostacyclin signalling through prostacyclin receptor / WD40-repeat-containing domain / Calcitonin, conserved site / Activation of the phototransduction cascade / G-protein beta WD-40 repeat / Calcitonin/adrenomedullin / Calcitonin-like / P-loop containing nucleoside triphosphate hydrolase / G protein alpha subunit, helical insertion / Receptor activity modifying protein / WD40-repeat-containing domain superfamily / GPCR, family 2, secretin-like / Glucagon signaling in metabolic regulation / Inactivation, recovery and regulation of the phototransduction cascade / PKA activation in glucagon signalling / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Olfactory Signaling Pathway / ADP signalling through P2Y purinoceptor 12 / G-protein alpha subunit, group S / Guanine nucleotide binding protein (G-protein), alpha subunit / GPCR, family 2, calcitonin gene-related peptide, type 1 receptor / G-protein, beta subunit / WD40 repeat / Calcitonin peptide-like / G-protein, gamma subunit / G beta:gamma signalling through PI3Kgamma / GPCR, family 2, extracellular hormone receptor domain / GPCR, family 2, calcitonin receptor family / G-protein gamma-like domain superfamily / WD40 repeat, conserved site / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / Vasopressin regulates renal water homeostasis via Aquaporins / Thrombin signalling through proteinase activated receptors (PARs) / Presynaptic function of Kainate receptors / Hedgehog 'off' state / G-protein coupled receptors family 2 signature 1. / RAMP domain superfamily / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Calcitonin / CGRP / IAPP family signature. / Trp-Asp (WD) repeats signature. / G-protein gamma subunit domain profile. / Trp-Asp (WD) repeats profile. / G-protein coupled receptors family 2 profile 1. / G-protein coupled receptors family 2 profile 2. / Trp-Asp (WD) repeats circular profile. / Thromboxane signalling through TP receptor / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Receptor activity modifying family / G-protein alpha subunit / 7 transmembrane receptor (Secretin family) / G alpha (q) signalling events / G alpha (12/13) signalling events / G beta:gamma signalling through PLC beta / Glucagon-type ligand receptors / Calcitonin / CGRP / IAPP family / WD domain, G-beta repeat / G-protein activation / G alpha (s) signalling events / ADP signalling through P2Y purinoceptor 1 / Calcitonin-like ligand receptors / G alpha (z) signalling events / Hormone receptor domain / G alpha (i) signalling events / GGL domain / positive regulation of interleukin-1 alpha production / neurological system process involved in regulation of systemic arterial blood pressure / calcitonin gene-related peptide binding / calcitonin gene-related peptide receptor signaling pathway / CGRP receptor complex / positive regulation of protein glycosylation / adrenomedullin receptor activity / adrenomedullin binding / amylin receptor activity / amylin receptor complex 1 / adrenomedullin receptor complex / calcitonin receptor activity / adrenomedullin receptor signaling pathway / calcitonin gene-related peptide receptor activity / cellular response to sucrose stimulus / amylin receptor signaling pathway / intracellular transport / intrinsic component of membrane / hair follicle placode formation / cardiac muscle cell apoptotic process / cellular response to catecholamine stimulus / negative regulation of calcium ion transport into cytosol / regulation of G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway / G protein-coupled receptor internalization / G protein-coupled acetylcholine receptor signaling pathway
Function and homology information
SourceHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsLiang YL / Khoshouei M / Deganutti G / Glukhova A / Koole C / Peat TS / Radjainia M / Plitzko JM / Baumeister W / Miller LJ / Hay DL / Christopoulos A / Reynolds CA / Wootten D / Sexton PM
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of the active, G-protein complexed, human CGRP receptor.
Authors: Yi-Lynn Liang / Maryam Khoshouei / Giuseppe Deganutti / Alisa Glukhova / Cassandra Koole / Thomas S Peat / Mazdak Radjainia / Jürgen M Plitzko / Wolfgang Baumeister / Laurence J Miller / Deborah L Hay / Arthur Christopoulos / Christopher A Reynolds / Denise Wootten / Patrick M Sexton
Validation ReportPDB-ID: 6e3y

SummaryFull reportAbout validation report
DateDeposition: Jul 16, 2018 / Header (metadata) release: Aug 1, 2018 / Map release: Sep 19, 2018 / Last update: Oct 10, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6e3y
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8978.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:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.071706764 - 0.17341213
Average (Standard dev.)0.0015997638 (0.008368622)
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-0.0720.1730.002

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Supplemental data

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Sample components

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Entire Complex of a full-length, active-state calcitonin gene-related pe...

EntireName: Complex of a full-length, active-state calcitonin gene-related peptide receptor with calcitonin gene-related peptide ligand, heterotrimeric Gs protein and nanobody35
Number of components: 8

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

ProteinName: Complex of a full-length, active-state calcitonin gene-related peptide receptor with calcitonin gene-related peptide ligand, heterotrimeric Gs protein and nanobody35
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #2: protein, Calcitonin gene-related peptide 1

ProteinName: Calcitonin gene-related peptide 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.790315 kDa
SourceSpecies: Homo sapiens (human)

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Component #3: protein, Nanobody 35

ProteinName: Nanobody 35Single-domain antibody / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.122602 kDa
SourceSpecies: Lama glama (llama)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: 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: 45.621902 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: 38.48768 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: 7.850056 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #7: protein, Calcitonin gene-related peptide type 1 receptor

ProteinName: Calcitonin gene-related peptide type 1 receptor / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.218055 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #8: protein, Receptor activity-modifying protein 1

ProteinName: Receptor activity-modifying protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.048561 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: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: NITROGEN / 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: OTHER
LensMagnification: 47170.0 X (calibrated) / 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: 407000
3D reconstructionCTF correction: phase plate CTF correction / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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