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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.1126/science.aaz8995
  • Primary Citation of Related Structures:  
    6W25

  • 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 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

    iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Melanocortin receptor 4,GlgA glycogen synthase,Melanocortin receptor 4535Homo sapiensPyrococcus abyssi GE5Mutation(s): 5 
Gene Names: MC4RPAB2292
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V2J8 
Go to UniProtKB:  Q9V2J8
Find proteins for P32245 (Homo sapiens)
Explore P32245 
Go to UniProtKB:  P32245
PHAROS:  P32245
GTEx:  ENSG00000166603 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9V2J8P32245
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SHU91199synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLA
Query on OLA

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
NLE
Query on NLE
B
L-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

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references, Refinement description
  • Version 2.0: 2020-09-09
    Changes: Advisory, Atomic model, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 2.2: 2023-11-15
    Changes: Data collection, Derived calculations