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- EMDB-22962: CryoEM structure of the apo-CGRP receptor in a detergent micelle -

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Basic information

Entry
Database: EMDB / ID: EMD-22962
TitleCryoEM structure of the apo-CGRP receptor in a detergent micelle
Map data
Sampleapo CGRP receptor
  • Receptor activity-modifying protein 1
  • Calcitonin gene-related peptide type 1 receptor
Function / homology
Function and homology information


calcitonin gene-related peptide binding / positive regulation of protein glycosylation / amylin receptor activity / amylin receptor complex 1 / calcitonin gene-related peptide receptor signaling pathway / CGRP receptor complex / adrenomedullin binding / adrenomedullin receptor complex / adrenomedullin receptor activity / adrenomedullin receptor signaling pathway ...calcitonin gene-related peptide binding / positive regulation of protein glycosylation / amylin receptor activity / amylin receptor complex 1 / calcitonin gene-related peptide receptor signaling pathway / CGRP receptor complex / adrenomedullin binding / adrenomedullin receptor complex / adrenomedullin receptor activity / adrenomedullin receptor signaling pathway / calcitonin receptor activity / cellular response to sucrose stimulus / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / negative regulation of smooth muscle contraction / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G protein-coupled peptide receptor activity / coreceptor activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to hormone stimulus / protein localization to plasma membrane / calcium ion transport / receptor internalization / intracellular protein transport / positive regulation of smooth muscle cell proliferation / negative regulation of inflammatory response / protein transport / heart development / angiogenesis / positive regulation of protein binding / lysosome / cell surface receptor signaling pathway / receptor complex / endosome / G protein-coupled receptor signaling pathway / endoplasmic reticulum / cell surface / integral component of plasma membrane / extracellular space / plasma membrane / cytoplasm
GPCR, family 2, calcitonin receptor family / GPCR, family 2, extracellular hormone receptor domain / RAMP domain superfamily / GPCR family 2, extracellular hormone receptor domain superfamily / GPCR, family 2, secretin-like, conserved site / GPCR, family 2-like / Receptor activity modifying protein / GPCR, family 2, calcitonin gene-related peptide, type 1 receptor / GPCR, family 2, secretin-like
Receptor activity-modifying protein 1 / Calcitonin gene-related peptide type 1 receptor
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsBelousoff MJ / Danev R
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)1065410 Australia
National Health and Medical Research Council (NHMRC, Australia)1126857 Australia
National Health and Medical Research Council (NHMRC, Australia)1055134 Australia
CitationJournal: Science / Year: 2021
Title: Structure and dynamics of the CGRP receptor in apo and peptide-bound forms.
Authors: Tracy M Josephs / Matthew J Belousoff / Yi-Lynn Liang / Sarah J Piper / Jianjun Cao / Daniel J Garama / Katie Leach / Karen J Gregory / Arthur Christopoulos / Debbie L Hay / Radostin Danev / ...Authors: Tracy M Josephs / Matthew J Belousoff / Yi-Lynn Liang / Sarah J Piper / Jianjun Cao / Daniel J Garama / Katie Leach / Karen J Gregory / Arthur Christopoulos / Debbie L Hay / Radostin Danev / Denise Wootten / Patrick M Sexton /
Abstract: G protein-coupled receptors (GPCRs) are key regulators of information transmission between cells and organs. Despite this, we have only limited understanding of the behavior of GPCRs in the apo state ...G protein-coupled receptors (GPCRs) are key regulators of information transmission between cells and organs. Despite this, we have only limited understanding of the behavior of GPCRs in the apo state and the conformational changes upon agonist binding that lead to G protein recruitment and activation. We expressed and purified unmodified apo and peptide-bound calcitonin gene-related peptide (CGRP) receptors to determine their cryo-EM structures and complemented these with analysis of protein conformational dynamics using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and 3D variance analysis of the cryo-EM data. Together with our previously published structure of the active, Gs-bound, CGRP receptor complex, our work provides important insight into mechanisms of class B1 GPCR activation.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionNov 6, 2020-
Header (metadata) releaseFeb 24, 2021-
Map releaseFeb 24, 2021-
UpdateMar 3, 2021-
Current statusMar 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.277
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.277
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7knt
  • Surface level: 0.277
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7knt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22962.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.)
0.83 Å/pix.
x 240 pix.
= 199.2 Å
0.83 Å/pix.
x 240 pix.
= 199.2 Å
0.83 Å/pix.
x 240 pix.
= 199.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.277 / Movie #1: 0.277
Minimum - Maximum-0.7466571 - 1.1903777
Average (Standard dev.)-0.0004136011 (±0.03664197)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 199.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z199.200199.200199.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.7471.190-0.000

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Supplemental data

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Segmentation: #1

Fileemd_22962_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Map refined using the SIDESPLITTER reconstruction in combination...

Fileemd_22962_additional_1.map
AnnotationMap refined using the SIDESPLITTER reconstruction in combination with RELION 3.1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map1

Fileemd_22962_half_map_1.map
AnnotationHalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map2

Fileemd_22962_half_map_2.map
AnnotationHalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire apo CGRP receptor

EntireName: apo CGRP receptor / Number of components: 3

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Component #1: protein, apo CGRP receptor

ProteinName: apo CGRP receptor / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #2: protein, Receptor activity-modifying protein 1

ProteinName: Receptor activity-modifying protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.066701 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: protein, Calcitonin gene-related peptide type 1 receptor

ProteinName: Calcitonin gene-related peptide type 1 receptor / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.27452 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
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 57.3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 542650
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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