7F16

Cryo-EM structure of parathyroid hormone receptor type 2 in complex with a tuberoinfundibular peptide of 39 residues and G protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Molecular insights into differentiated ligand recognition of the human parathyroid hormone receptor 2.

Wang, X.Cheng, X.Zhao, L.Wang, Y.Ye, C.Zou, X.Dai, A.Cong, Z.Chen, J.Zhou, Q.Xia, T.Jiang, H.Xu, H.E.Yang, D.Wang, M.W.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2101279118
  • Primary Citation of Related Structures:  
    7F16

  • PubMed Abstract: 

    The parathyroid hormone receptor 2 (PTH2R) is a class B1 G protein-coupled receptor (GPCR) involved in the regulation of calcium transport, nociception mediation, and wound healing. Naturally occurring mutations in PTH2R were reported to cause hereditary diseases, including syndromic short stature. Here, we report the cryogenic electron microscopy structure of PTH2R bound to its endogenous ligand, tuberoinfundibular peptide (TIP39), and a heterotrimeric G s protein at a global resolution of 2.8 Å. The structure reveals that TIP39 adopts a unique loop conformation at the N terminus and deeply inserts into the orthosteric ligand-binding pocket in the transmembrane domain. Molecular dynamics simulation and site-directed mutagenesis studies uncover the basis of ligand specificity relative to three PTH2R agonists, TIP39, PTH, and PTH-related peptide. We also compare the action of TIP39 with an antagonist lacking six residues from the peptide N terminus, TIP(7-39), which underscores the indispensable role of the N terminus of TIP39 in PTH2R activation. Additionally, we unveil that a disease-associated mutation G258D significantly diminished cAMP accumulation induced by TIP39. Together, these results not only provide structural insights into ligand specificity and receptor activation of class B1 GPCRs but also offer a foundation to systematically rationalize the available pharmacological data to develop therapies for various disorders associated with PTH2R.


  • Organizational Affiliation

    The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Parathyroid hormone 2 receptorA [auth R]434Homo sapiensMutation(s): 0 
Gene Names: PTH2RPTHR2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P49190 (Homo sapiens)
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Go to UniProtKB:  P49190
PHAROS:  P49190
GTEx:  ENSG00000144407 
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UniProt GroupP49190
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tuberoinfundibular peptide of 39 residuesB [auth P]39Homo sapiensMutation(s): 0 
Gene Names: PTH2TIP39TIPF39
Membrane Entity: Yes 
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Find proteins for Q96A98 (Homo sapiens)
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Go to UniProtKB:  Q96A98
PHAROS:  Q96A98
GTEx:  ENSG00000142538 
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UniProt GroupQ96A98
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortC [auth A]394Homo sapiensMutation(s): 8 
Gene Names: GNASGNAS1GSP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth B]371Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus)
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UniProt GroupP54311
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth G]71Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P63212 (Bos taurus)
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UniProt GroupP63212
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody-35F [auth N]140Lama glamaMutation(s): 0 
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
G [auth R],
H [auth R],
I [auth R],
J [auth R]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
PLM
Query on PLM

Download Ideal Coordinates CCD File 
K [auth R]
L [auth R]
M [auth R]
N [auth R]
O [auth R]
K [auth R],
L [auth R],
M [auth R],
N [auth R],
O [auth R],
P [auth R]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81872915
National Natural Science Foundation of China (NSFC)China82073904
National Natural Science Foundation of China (NSFC)China32071203
National Natural Science Foundation of China (NSFC)China81773792
National Natural Science Foundation of China (NSFC)China81973373
National Natural Science Foundation of China (NSFC)China21704064
Ministry of Science and Technology (MoST, China)China2018YFA0507002

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release