7UM6 | pdb_00007um6

CryoEM structure of Go-coupled 5-HT5AR in complex with Lisuride


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7UM6

This is version 1.3 of the entry. See complete history

Literature

Inactive and active state structures template selective tools for the human 5-HT 5A receptor.

Zhang, S.Chen, H.Zhang, C.Yang, Y.Popov, P.Liu, J.Krumm, B.E.Cao, C.Kim, K.Xiong, Y.Katritch, V.Shoichet, B.K.Jin, J.Fay, J.F.Roth, B.L.

(2022) Nat Struct Mol Biol 29: 677-687

  • DOI: https://doi.org/10.1038/s41594-022-00796-6
  • Primary Citation Related Structures: 
    7UM4, 7UM5, 7UM6, 7UM7

  • PubMed Abstract: 

    Serotonin receptors are important targets for established therapeutics and drug development as they are expressed throughout the human body and play key roles in cell signaling. There are 12 serotonergic G protein-coupled receptor members encoded in the human genome, of which the 5-hydroxytryptamine (5-HT) 5A receptor (5-HT 5A R) is the least understood and lacks selective tool compounds. Here, we report four high-resolution (2.73-2.80 Å) structures of human 5-HT 5A Rs, including an inactive state structure bound to an antagonist AS2674723 by crystallization and active state structures bound to a partial agonist lisuride and two full agonists, 5-carboxamidotryptamine (5-CT) and methylergometrine, by cryo-EM. Leveraging the new structures, we developed a highly selective and potent antagonist for 5-HT 5A R. Collectively, these findings both enhance our understanding of this enigmatic receptor and provide a roadmap for structure-based drug discovery for 5-HT 5A R.


  • Organizational Affiliation
    • Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Macromolecule Content 

  • Total Structure Weight: 134.21 kDa 
  • Atom Count: 8,175 
  • Modeled Residue Count: 1,094 
  • Deposited Residue Count: 1,212 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 5A326Homo sapiensMutation(s): 1 
Gene Names: HTR5A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P47898 (Homo sapiens)
Explore P47898 
Go to UniProtKB:  P47898
PHAROS:  P47898
GTEx:  ENSG00000157219 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47898
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
miniGo protein225Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1339Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62873
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59768
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Single-chain variable fragment scFv16251Mus musculusMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H8G
(Subject of Investigation/LOI)

Query on H8G



Download:Ideal Coordinates CCD File
F [auth A]N,N-diethyl-N'-[(8alpha)-6-methyl-9,10-didehydroergolin-8-yl]urea
C20 H26 N4 O
BKRGVLQUQGGVSM-KBXCAEBGSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
H8G BindingDB:  7UM6 Ki: 3.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesRO1MH112205
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesU24DK1169195

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-05-21
    Changes: Data collection