Generic GPCR residue numbers - aligning topology maps while minding the gaps

Vignir Isberg; Chris de Graaf; Andrea Bortolato; Vadim Cherezov; Vsevolod Katritch; Fiona H Marshall; Stefan Mordalski; Jean-Philippe Pin; Raymond C Stevens; Gerrit Vriend; David E Gloriam

doi:10.1016/j.tips.2014.11.001

Generic GPCR residue numbers - aligning topology maps while minding the gaps

Vignir Isberg, Chris de Graaf, Andrea Bortolato, Vadim Cherezov, Vsevolod Katritch, Fiona H Marshall, Stefan Mordalski, Jean-Philippe Pin, Raymond C Stevens, Gerrit Vriend, David E Gloriam

196 Citations (Scopus)

259 Downloads (Pure)

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.

Original language	English
Journal	Trends in Pharmacological Sciences
Volume	36
Issue number	1
Pages (from-to)	22-31
Number of pages	10
ISSN	0165-6147
DOIs	https://doi.org/10.1016/j.tips.2014.11.001
Publication status	Published - 1 Jan 2015

Access to Document

10.1016/j.tips.2014.11.001

TIPS_Revised_ProofsAccepted author manuscript, 2.81 MBLicence: Unspecified

Cite this

@article{af5af5c8a03443348c88eced69991f30,

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.",

author = "Vignir Isberg and {de Graaf}, Chris and Andrea Bortolato and Vadim Cherezov and Vsevolod Katritch and Marshall, {Fiona H} and Stefan Mordalski and Jean-Philippe Pin and Stevens, {Raymond C} and Gerrit Vriend and Gloriam, {David E}",

year = "2015",

month = jan,

day = "1",

doi = "10.1016/j.tips.2014.11.001",

language = "English",

volume = "36",

pages = "22--31",

journal = "Trends in Pharmacological Sciences",

issn = "0165-6147",

publisher = "Elsevier Ltd. * Trends Journals",

number = "1",

}

TY - JOUR

T1 - Generic GPCR residue numbers - aligning topology maps while minding the gaps

AU - Isberg, Vignir

AU - de Graaf, Chris

AU - Bortolato, Andrea

AU - Cherezov, Vadim

AU - Katritch, Vsevolod

AU - Marshall, Fiona H

AU - Mordalski, Stefan

AU - Pin, Jean-Philippe

AU - Stevens, Raymond C

AU - Vriend, Gerrit

AU - Gloriam, David E

PY - 2015/1/1

Y1 - 2015/1/1

N2 - 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.

AB - 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.

U2 - 10.1016/j.tips.2014.11.001

DO - 10.1016/j.tips.2014.11.001

M3 - Journal article

C2 - 25541108

SN - 0165-6147

VL - 36

SP - 22

EP - 31

JO - Trends in Pharmacological Sciences

JF - Trends in Pharmacological Sciences

IS - 1

ER -

Generic GPCR residue numbers - aligning topology maps while minding the gaps

Abstract

Access to Document

Fingerprint

Cite this