5FBH

Crystal structure of the extracellular domain of human calcium sensing receptor with bound Gd3+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for regulation of human calcium-sensing receptor by magnesium ions and an unexpected tryptophan derivative co-agonist.

Zhang, C.Zhang, T.Zou, J.Miller, C.L.Gorkhali, R.Yang, J.Y.Schilmiller, A.Wang, S.Huang, K.Brown, E.M.Moremen, K.W.Hu, J.Yang, J.J.

(2016) Sci Adv 2: e1600241-e1600241

  • DOI: https://doi.org/10.1126/sciadv.1600241
  • Primary Citation of Related Structures:  
    5FBH, 5FBK

  • PubMed Abstract: 

    Ca(2+)-sensing receptors (CaSRs) modulate calcium and magnesium homeostasis and many (patho)physiological processes by responding to extracellular stimuli, including divalent cations and amino acids. We report the first crystal structure of the extracellular domain (ECD) of human CaSR bound with Mg(2+) and a tryptophan derivative ligand at 2.1 Å. The structure reveals key determinants for cooperative activation by metal ions and aromatic amino acids. The unexpected tryptophan derivative was bound in the hinge region between two globular ECD subdomains, and represents a novel high-affinity co-agonist of CaSR. The dissection of structure-function relations by mutagenesis, biochemical, and functional studies provides insights into the molecular basis of human diseases arising from CaSR mutations. The data also provide a novel paradigm for understanding the mechanism of CaSR-mediated signaling that is likely shared by the other family C GPCR [G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptor] members and can facilitate the development of novel CaSR-based therapeutics.


  • Organizational Affiliation

    Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street, Atlanta, GA 30303, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular calcium-sensing receptorA [auth B],
B [auth A]
568Homo sapiensMutation(s): 0 
Gene Names: CASRGPRC2APCAR1
UniProt & NIH Common Fund Data Resources
Find proteins for P41180 (Homo sapiens)
Explore P41180 
Go to UniProtKB:  P41180
PHAROS:  P41180
GTEx:  ENSG00000036828 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41180
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P41180-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth B]
I [auth B]
J [auth B]
P [auth A]
Q [auth A]
H [auth B],
I [auth B],
J [auth B],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
TCR
Query on TCR

Download Ideal Coordinates CCD File 
K [auth B],
T [auth A]
CYCLOMETHYLTRYPTOPHAN
C12 H12 N2 O2
FSNCEEGOMTYXKY-JTQLQIEISA-N
GD3
Query on GD3

Download Ideal Coordinates CCD File 
C [auth B],
L [auth A]
GADOLINIUM ION
Gd
RJOJUSXNYCILHH-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
F [auth B],
N [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth B],
O [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth B],
E [auth B],
M [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A [auth B],
B [auth A]
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.107α = 90
b = 83.106β = 105.15
c = 94.47γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary