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- EMDB-63682: Cryo-EM structure of the human glucagon receptor (GCGR) in ligand... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63682
TitleCryo-EM structure of the human glucagon receptor (GCGR) in ligand free state resolved via the fusion/crosslinking strategy
Map data
Sample
  • Complex: Apo GCGR-GFP10-11:GFP1-9:GFP-clamp E186C complex
    • Protein or peptide: Glucagon receptor
    • Protein or peptide: Green fluorescent protein
    • Protein or peptide: GFP-clamp E186C
Keywordsthe human glucagon receptor (GCGR) / Fusion/crosslinking strategy / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsHan SC / Li MH
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure determination of GPCRs with disulfide-crosslinked fusion protein
Authors: Han SC / Li MH
History
DepositionMar 10, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63682.png

Downloads & links

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Map

FileDownload / File: emd_63682.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-4.2125125 - 5.652564
Average (Standard dev.)-0.0005028501 (±0.093222976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63682_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63682_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apo GCGR-GFP10-11:GFP1-9:GFP-clamp E186C complex

EntireName: Apo GCGR-GFP10-11:GFP1-9:GFP-clamp E186C complex
Components
  • Complex: Apo GCGR-GFP10-11:GFP1-9:GFP-clamp E186C complex
    • Protein or peptide: Glucagon receptor
    • Protein or peptide: Green fluorescent protein
    • Protein or peptide: GFP-clamp E186C

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Supramolecule #1: Apo GCGR-GFP10-11:GFP1-9:GFP-clamp E186C complex

SupramoleculeName: Apo GCGR-GFP10-11:GFP1-9:GFP-clamp E186C complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glucagon receptor

MacromoleculeName: Glucagon receptor / type: protein_or_peptide / ID: 1
Details: Author stated 335-364 is GFP10-11.,Author stated 335-364 is GFP10-11.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.980281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AQVMDFLFEK WKLYGDQCHH NLSLLPPPTE LVCNRTFDKY SCWPDTPANT TANISCPWYL PWHHKVQHRF VFKRCGPDGQ WVRGPRGQP WRDASQCQMD GEEIEVQKEV AKMYSSFQVM YTVGYSLSLG ALLLALAILG GLSKLHCTRN AIHANLFASF V LKASSVLV ...String:
AQVMDFLFEK WKLYGDQCHH NLSLLPPPTE LVCNRTFDKY SCWPDTPANT TANISCPWYL PWHHKVQHRF VFKRCGPDGQ WVRGPRGQP WRDASQCQMD GEEIEVQKEV AKMYSSFQVM YTVGYSLSLG ALLLALAILG GLSKLHCTRN AIHANLFASF V LKASSVLV IDGLLRTRYS QKIGDDLSVS TWLSDGAVAG CRVAAVFMQY GIVANYCWLL VEGLYLHNLL GLACLPERSF FS LYLGIGW GAPMLFVVPW AVVKCLFENV QCWTSNDNMG FWWILRFPVF LAILINFFIF VRIVQLLRRQ LGHYLSTQTS LSK DLNEKR DHMVLLEFVT AAGLQKEFRL AKSTLTLIPL LGVHEVVFAF VTDEHAQGTL RSAKLFFDLF LSSFQGLLVA VLYC FLNKE VQSELRRRWH RWRLGKVLWE ERNTSNHRAS SSPGHGPPSK ELQFGRGGGS QDSSAETPLA GGLPRLAESP F

UniProtKB: Glucagon receptor, Glucagon receptor

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Macromolecule #2: Green fluorescent protein

MacromoleculeName: Green fluorescent protein / type: protein_or_peptide / ID: 2 / Details: Author stated 2-3 is GFP1-9. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 22.388293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGTRKGEELF TGVVPILIEL DGDVNGHKFS VRGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTL(CRO)VQC FSRYPD HMK RHDFFKSAMP EGYVQERTIY FKDDGTYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNFNSHN VYIMADK QN NGIKANFKIR ...String:
MGTRKGEELF TGVVPILIEL DGDVNGHKFS VRGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTL(CRO)VQC FSRYPD HMK RHDFFKSAMP EGYVQERTIY FKDDGTYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNFNSHN VYIMADK QN NGIKANFKIR HNVEDGSVQL ADHYQQNTPI GDGPVLLP

UniProtKB: Green fluorescent protein

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Macromolecule #3: GFP-clamp E186C

MacromoleculeName: GFP-clamp E186C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 31.038664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DLGKKLLEAA RAGQDDEVRI LMANGADVNA ADDVGVTPLH LAAQRGHLEI VEVLLKYGAD VNAADLWGQT PLHLAATAGH LEIVEVLLK NGADVNARDN IGHTPLHLAA WAGHLEIVEV LLKYGADVNA QDKFGKTPFD LAIDNGNEDI AEVLQKAAGG G SGGGDVNA ...String:
DLGKKLLEAA RAGQDDEVRI LMANGADVNA ADDVGVTPLH LAAQRGHLEI VEVLLKYGAD VNAADLWGQT PLHLAATAGH LEIVEVLLK NGADVNARDN IGHTPLHLAA WAGHLEIVEV LLKYGADVNA QDKFGKTPFD LAIDNGNEDI AEVLQKAAGG G SGGGDVNA YDEVGWTPLH KAAWGHLCKV EDLLKNGADV NAADIDGYTP LHLAAFSGHL EIVEVLLKYG ADVNADDQAG FT PLHLAAI FGHLEIVEVL LKNGADVNAQ DKFGKTPFDL AIDNGNEDIA EVLQKAA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 107457
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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