6W25

Crystal structure of the Melanocortin-4 Receptor (MC4R) in complex with SHU9119


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Determination of the melanocortin-4 receptor structure identifies Ca2+as a cofactor for ligand binding.

Yu, J.Gimenez, L.E.Hernandez, C.C.Wu, Y.Wein, A.H.Han, G.W.McClary, K.Mittal, S.R.Burdsall, K.Stauch, B.Wu, L.Stevens, S.N.Peisley, A.Williams, S.Y.Chen, V.Millhauser, G.L.Zhao, S.Cone, R.D.Stevens, R.C.

(2020) Science 368: 428-433

  • DOI: 10.1126/science.aaz8995
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The melanocortin-4 receptor (MC4R) is involved in energy homeostasis and is an important drug target for syndromic obesity. We report the structure of the antagonist SHU9119-bound human MC4R at 2.8-angstrom resolution. Ca 2+ is identified ...

    The melanocortin-4 receptor (MC4R) is involved in energy homeostasis and is an important drug target for syndromic obesity. We report the structure of the antagonist SHU9119-bound human MC4R at 2.8-angstrom resolution. Ca 2+ is identified as a cofactor that is complexed with residues from both the receptor and peptide ligand. Extracellular Ca 2+ increases the affinity and potency of the endogenous agonist α-melanocyte-stimulating hormone at the MC4R by 37- and 600-fold, respectively. The ability of the MC4R crystallized construct to couple to ion channel Kir7.1, while lacking cyclic adenosine monophosphate stimulation, highlights a heterotrimeric GTP-binding protein (G protein)-independent mechanism for this signaling modality. MC4R is revealed as a structurally divergent G protein-coupled receptor (GPCR), with more similarity to lipidic GPCRs than to the homologous peptidic GPCRs.


    Organizational Affiliation

    Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Melanocortin receptor 4,GlgA glycogen synthase,Melanocortin receptor 4
A
535Homo sapiensPyrococcus abyssi GE5Mutation(s): 5 
Gene Names: MC4R
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Melanocortin-4 Receptor (MC4R) in complex with antagonist SHU9119
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V2J8
Find proteins for P32245 (Homo sapiens)
Go to UniProtKB:  P32245
NIH Common Fund Data Resources
PHAROS  P32245
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SHU9119
B
9synthetic constructMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLA
Query on OLA

Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
AL-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
NLE
Query on NLE
BL-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.91α = 90
b = 44.49β = 97.47
c = 88.05γ = 90
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references, Refinement description