Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 232.17 kDa 
• Atom Count: 15041 
• Modelled Residue Count: 1930 
• Deposited Residue Count: 2038 
• Unique protein chains: 3

5XF1

Structure of the Full-length glucagon class B G protein-coupled receptor

• PDB DOI: 10.2210/pdb5XF1/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Escherichia virus T4
• Expression System: Spodoptera frugiperda, Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2017-04-06 Released: 2017-05-24 
• Deposition Author(s): Zhang, H., Qiao, A., Yang, D., Yang, L., Dai, A., de Graaf, C., Reedtz-Runge, S., Dharmarajan, V., Zhang, H., Han, G.W., Grant, T., Sierra, R., Weierstall, U., Nelson, G., Liu, W., Wu, Y., Ma, L., Cai, X., Lin, G., Wu, X., Geng, Z., Dong, Y., Song, G., Griffin, P., Lau, J., Cherezov, V., Yang, H., Hanson, M., Stevens, R., Jiang, H., Wang, M., Zhao, Q., Wu, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.231 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Structure of the full-length glucagon class B G-protein-coupled receptor.

Zhang, H., Qiao, A., Yang, D., Yang, L., Dai, A., de Graaf, C., Reedtz-Runge, S., Dharmarajan, V., Zhang, H., Han, G.W., Grant, T.D., Sierra, R.G., Weierstall, U., Nelson, G., Liu, W., Wu, Y., Ma, L., Cai, X., Lin, G., Wu, X., Geng, Z., Dong, Y., Song, G., Griffin, P.R., Lau, J., Cherezov, V., Yang, H., Hanson, M.A., Stevens, R.C., Zhao, Q., Jiang, H., Wang, M.W., Wu, B.

(2017) Nature 546: 259-264

• PubMed: 28514451 
• DOI: 10.1038/nature22363
• Primary Citation of Related Structures:  
  5XEZ, 5XF1


• PubMed Abstract: 
  

The human glucagon receptor, GCGR, belongs to the class B G-protein-coupled receptor family and plays a key role in glucose homeostasis and the pathophysiology of type 2 diabetes. Here we report the 3.0 Å crystal structure of full-length GCGR containing both the extracellular domain and transmembrane domain in an inactive conformation. The two domains are connected by a 12-residue segment termed the stalk, which adopts a β-strand conformation, instead of forming an α-helix as observed in the previously solved structure of the GCGR transmembrane domain. The first extracellular loop exhibits a β-hairpin conformation and interacts with the stalk to form a compact β-sheet structure. Hydrogen-deuterium exchange, disulfide crosslinking and molecular dynamics studies suggest that the stalk and the first extracellular loop have critical roles in modulating peptide ligand binding and receptor activation. These insights into the full-length GCGR structure deepen our understanding of the signalling mechanisms of class B G-protein-coupled receptors.

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Organizational Affiliation: 

CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucagon receptor,Endolysin,Glucagon receptor	A, B	574	Homo sapiens, Escherichia virus T4	Mutation(s): 2  Gene Names: GCGR, E, T4Tp126 EC: 3.2.1.17 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P47871 (Homo sapiens) Explore P47871  Go to UniProtKB:  P47871
PHAROS:  P47871
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
UniProt Groups	P47871P00720

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody mAb1 Heavy chain	C, E [auth H]	231	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody mAb1 Light chain	D, F [auth L]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth E], H [auth F], I [auth G], J [auth I], L [auth K]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth J]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
97V	M [auth A], O [auth B]	4-{[(4-cyclohexylphenyl){[3-(methylsulfonyl)phenyl]carbamoyl}amino]methyl}-N-(1H-tetrazol-5-yl)benzamide C29 H31 N7 O4 S PPTKULJUDJWTSA-UHFFFAOYSA-N
NAG	N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	K [auth J]	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.231 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.46	α = 90
b = 248.79	β = 90.16
c = 93.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-04-06 
• Released Date: 2017-05-24 
Deposition Author(s): Zhang, H., Qiao, A., Yang, D., Yang, L., Dai, A., de Graaf, C., Reedtz-Runge, S., Dharmarajan, V., Zhang, H., Han, G.W., Grant, T., Sierra, R., Weierstall, U., Nelson, G., Liu, W., Wu, Y., Ma, L., Cai, X., Lin, G., Wu, X., Geng, Z., Dong, Y., Song, G., Griffin, P., Lau, J., Cherezov, V., Yang, H., Hanson, M., Stevens, R., Jiang, H., Wang, M., Zhao, Q., Wu, B.

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2017-06-14
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary