7ZL9

Crystal structure of human GPCR Niacin receptor (HCA2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the human niacin receptor HCA2-G i signalling complex.

Yang, Y.Kang, H.J.Gao, R.Wang, J.Han, G.W.DiBerto, J.F.Wu, L.Tong, J.Qu, L.Wu, Y.Pileski, R.Li, X.Zhang, X.C.Zhao, S.Kenakin, T.Wang, Q.Stevens, R.C.Peng, W.Roth, B.L.Rao, Z.Liu, Z.J.

(2023) Nat Commun 14: 1692-1692

  • DOI: https://doi.org/10.1038/s41467-023-37177-6
  • Primary Citation of Related Structures:  
    7XK2, 7ZL9, 7ZLY

  • PubMed Abstract: 

    The hydroxycarboxylic acid receptor 2 (HCA2) agonist niacin has been used as treatment for dyslipidemia for several decades albeit with skin flushing as a common side-effect in treated individuals. Extensive efforts have been made to identify HCA2 targeting lipid lowering agents with fewer adverse effects, despite little being known about the molecular basis of HCA2 mediated signalling. Here, we report the cryo-electron microscopy structure of the HCA2-G i signalling complex with the potent agonist MK-6892, along with crystal structures of HCA2 in inactive state. These structures, together with comprehensive pharmacological analysis, reveal the ligand binding mode and activation and signalling mechanisms of HCA2. This study elucidates the structural determinants essential for HCA2 mediated signalling and provides insights into ligand discovery for HCA2 and related receptors.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxycarboxylic acid receptor 2,Soluble cytochrome b562431Homo sapiensEscherichia coli
This entity is chimeric
Mutation(s): 0 
Gene Names: HCAR2GPR109AHCA2HM74ANIACR1cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for Q8TDS4 (Homo sapiens)
Explore Q8TDS4 
Go to UniProtKB:  Q8TDS4
PHAROS:  Q8TDS4
GTEx:  ENSG00000182782 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7Q8TDS4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
G [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA
Query on OLA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.88α = 90
b = 81.99β = 90
c = 85.78γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
BSSdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)ChinaGrant No. 2017YFC0840300
Chinese Academy of SciencesChinaGrant No. XDB08020200
National Science Foundation (NSF, China)China31330019
Ministry of Science and Technology (MoST, China)China2014CB910400 and 2015CB910104
National Natural Science Foundation of China (NSFC)China2016YCF0905902

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description