5XEZ

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

• PDB DOI: https://doi.org/10.2210/pdb5XEZ/pdb

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


• 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: 3.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Biological Assembly 1  

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.

Biological Assembly 2  

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.

Macromolecule Content

• Total Structure Weight: 231.98 kDa 
• Atom Count: 15,068 
• Modelled Residue Count: 1,934 
• Deposited Residue Count: 2,038 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucagon receptor,Endolysin,Glucagon receptor	A, B	574	Homo sapiens, Tequatrovirus 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 GTEx:  ENSG00000215644
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
UniProt Groups	P00720P47871

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	Length	2D Diagram	Glycosylation	3D Interactions
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], K [auth J]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
97V	M [auth A], P [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	L [auth A], N [auth B], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.61	α = 90
b = 245.33	β = 90.01
c = 96.15	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary