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- PDB-9m7g: Cryo-EM structure of the human glucagon receptor (GCGR) in ligand... -

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Basic information

Entry
Database: PDB / ID: 9m7g
TitleCryo-EM structure of the human glucagon receptor (GCGR) in ligand free state resolved via the fusion/crosslinking strategy
Components
  • GFP-clamp E186C
  • Glucagon receptor
  • Green fluorescent protein
KeywordsMEMBRANE PROTEIN / the human glucagon receptor (GCGR) / Fusion/crosslinking strategy
Function / homology
Function and homology information


glucagon receptor activity / response to starvation / peptide hormone binding / cellular response to glucagon stimulus / response to nutrient / guanyl-nucleotide exchange factor activity / bioluminescence / cellular response to starvation / generation of precursor metabolites and energy / regulation of blood pressure ...glucagon receptor activity / response to starvation / peptide hormone binding / cellular response to glucagon stimulus / response to nutrient / guanyl-nucleotide exchange factor activity / bioluminescence / cellular response to starvation / generation of precursor metabolites and energy / regulation of blood pressure / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / glucose homeostasis / Glucagon-type ligand receptors / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of gene expression / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, glucagon receptor / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. ...GPCR, family 2, glucagon receptor / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Glucagon receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Aequorea victoria (jellyfish)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsHan, S.C. / Li, M.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure determination of GPCRs with disulfide-crosslinked fusion protein
Authors: Han, S.C. / Li, M.H.
History
DepositionMar 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucagon receptor
B: Green fluorescent protein
C: GFP-clamp E186C


Theoretical massNumber of molelcules
Total (without water)107,4073
Polymers107,4073
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glucagon receptor / GL-R


Mass: 53980.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Author stated 335-364 is GFP10-11.,Author stated 335-364 is GFP10-11.
Source: (gene. exp.) Homo sapiens (human) / Gene: GCGR / Production host: Homo sapiens (human) / References: UniProt: P47871
#2: Protein Green fluorescent protein


Mass: 22388.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Author stated 2-3 is GFP1-9. / Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Homo sapiens (human) / References: UniProt: A0A059PIQ0
#3: Protein GFP-clamp E186C


Mass: 31038.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Apo GCGR-GFP10-11:GFP1-9:GFP-clamp E186C complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.19.2_4158model refinement
13RELION3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107457 / Symmetry type: POINT
RefinementHighest resolution: 3.38 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026099
ELECTRON MICROSCOPYf_angle_d0.5458273
ELECTRON MICROSCOPYf_dihedral_angle_d4.203806
ELECTRON MICROSCOPYf_chiral_restr0.037942
ELECTRON MICROSCOPYf_plane_restr0.0041057

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