6KS2

Structure of anti-Ghrelin receptor antibody

• PDB DOI: https://doi.org/10.2210/pdb6KS2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-23 Released: 2020-08-12 
• Deposition Author(s): Shiimura, Y., Horita, S., Asada, H., Hirata, K., Iwata, S., Kojima, M.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.233 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

Structure of an antagonist-bound ghrelin receptor reveals possible ghrelin recognition mode.

Shiimura, Y., Horita, S., Hamamoto, A., Asada, H., Hirata, K., Tanaka, M., Mori, K., Uemura, T., Kobayashi, T., Iwata, S., Kojima, M.

(2020) Nat Commun 11: 4160-4160

• PubMed: 32814772 
• DOI: https://doi.org/10.1038/s41467-020-17554-1
• Primary Citation of Related Structures:  
  6KO5, 6KS2


• PubMed Abstract: 
  

  Ghrelin is a gastric peptide hormone with important physiological functions. The unique feature of ghrelin is its Serine 3 acyl-modification, which is essential for ghrelin's activity. However, it remains to be elucidated why the acyl-modification of ghrelin is necessary for activity. To address these questions, we solved the crystal structure of the ghrelin receptor bound to antagonist. The ligand-binding pocket of the ghrelin receptor is bifurcated by a salt bridge between E124 and R283. A striking feature of the ligand-binding pocket of the ghrelin receptor is a wide gap (crevasse) between the TM6 and TM7 bundles that is rich in hydrophobic amino acids, including a cluster of phenylalanine residues. Mutagenesis analyses suggest that the interaction between the gap structure and the acyl acid moiety of ghrelin may participate in transforming the ghrelin receptor into an active conformation.

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Organizational Affiliation: 

Division of Molecular Genetics, Institute of Life Science, Kurume University, Fukuoka, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 95.22 kDa 
• Atom Count: 7,285 
• Modelled Residue Count: 872 
• Deposited Residue Count: 874 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab7881 Light Chain (FabL)	A, C	219	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab7881 Heavy Chain (FabH)	B, D	218	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.233 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.239	α = 90
b = 107.916	β = 90
c = 189.892	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Shiimura, Y., Horita, S., Asada, H., Hirata, K., Iwata, S., Kojima, M.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2020-08-26
  Changes: Database references
• Version 1.2: 2020-09-02
  Changes: Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary