title: Generic GPCR residue numbers - aligning topology maps while minding the gaps.
abstract: Generic residue numbers facilitate comparisons of, for example, mutational effects, ligand interactions, and structural motifs. The numbering scheme by Ballesteros and Weinstein for residues within the class A GPCRs (G protein-coupled receptors) has more than 1100 citations, and the recent crystal structures for classes B, C, and F now call for a community consensus in residue numbering within and across these classes. Furthermore, the structural era has uncovered helix bulges and constrictions that offset the generic residue numbers. The use of generic residue numbers depends on convenient access by pharmacologists, chemists, and structural biologists. We review the generic residue numbering schemes for each GPCR class, as well as a complementary structure-based scheme, and provide illustrative examples and GPCR database (GPCRDB) web tools to number any receptor sequence or structure.
authors.affiliation: Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Vignir
authors.initials: V
authors.lastname: Isberg
authors.affiliation: Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands.
authors.forename: Chris
authors.initials: C
authors.lastname: de Graaf
authors.affiliation: Heptares Therapeutics Ltd, Welwyn Garden City, UK.
authors.forename: Andrea
authors.initials: A
authors.lastname: Bortolato
authors.affiliation: The Bridge@USC, Department of Chemistry, University of Southern California, Los Angeles, CA 90089 USA.
authors.forename: Vadim
authors.initials: V
authors.lastname: Cherezov
authors.affiliation: The Bridge@USC, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 USA.
authors.forename: Vsevolod
authors.initials: V
authors.lastname: Katritch
authors.affiliation: Heptares Therapeutics Ltd, Welwyn Garden City, UK.
authors.forename: Fiona H
authors.initials: FH
authors.lastname: Marshall
authors.affiliation: Department of Medicinal Chemistry, Institute of Pharmacology, Polish Academy of Sciences, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Mordalski
authors.affiliation: Institute of Functional Genomics, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 5203, Universities Montpellier, Montpellier, France; Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 661, Montpellier, France.
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Pin
authors.affiliation: The Bridge@USC, Department of Chemistry, University of Southern California, Los Angeles, CA 90089 USA; The Bridge@USC, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 USA.
authors.forename: Raymond C
authors.initials: RC
authors.lastname: Stevens
authors.affiliation: Centre for Molecular and Biomolecular Informatics (CMBI), Radboudumc, Nijmegen, The Netherlands.
authors.forename: Gerrit
authors.initials: G
authors.lastname: Vriend
authors.affiliation: Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Electronic address: david.gloriam@sund.ku.dk.
authors.forename: David E
authors.initials: DE
authors.lastname: Gloriam
mesh_terms: D006801:Humans; D011487:Protein Conformation; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry* / Q000145:classification; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
chemical_list: D043562:Receptors, G-Protein-Coupled
keywords: G protein-coupled receptor; ligand binding; mutational effects; sequence alignments; structural motifs