6V2E

Crystal structure of the human CLR:RAMP2 extracellular domain heterodimer with bound high-affinity adrenomedullin S45R/K46L/S48G/Q50W variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Picomolar Affinity Antagonist and Sustained Signaling Agonist Peptide Ligands for the Adrenomedullin and Calcitonin Gene-Related Peptide Receptors.

Booe, J.M.Warner, M.L.Pioszak, A.A.

(2020) Acs Pharmacol Transl Sci 3: 759-772

  • DOI: https://doi.org/10.1021/acsptsci.0c00031
  • Primary Citation of Related Structures:  
    6V2E

  • PubMed Abstract: 

    The calcitonin receptor-like class B G protein-coupled receptor (CLR) mediates adrenomedullin (AM) and calcitonin gene-related peptide (CGRP) functions including vasodilation, cardioprotection, and nociception. Receptor activity-modifying proteins (RAMP1-3) form heterodimers with CLR and determine its peptide ligand selectivity through an unresolved mechanism. The CGRP (RAMP1:CLR) and AM (RAMP2/3:CLR) receptors are proven or promising drug targets, but short AM and CGRP plasma half-lives limit their therapeutic utility. Here, we used synthetic peptide combinatorial library and rational design approaches to probe the ligand selectivity determinants and develop truncated AM and CGRP antagonist variants with receptor extracellular domain binding affinities that were enhanced ∼1000-fold into the low nanomolar range. Receptor binding studies and a high-resolution crystal structure of a novel library-identified AM variant bound to the RAMP2-CLR extracellular domain complex explained the increased affinities and defined roles for AM Lys46 and RAMP modulation of CLR conformation in the ligand selectivity mechanism. In longer AM and CGRP scaffolds that also bind the CLR transmembrane domain, the variants generated picomolar affinity antagonists, one with an estimated 12.5 h CGRP receptor residence time, and sustained signaling agonists "ss-AM" and "ss-CGRP" that exhibited persistent cAMP signaling after ligand washout. Sustained signaling was demonstrated in primary human umbilical vein endothelial cells and the SK-N-MC cell line, which endogenously express AM and CGRP receptors, respectively. This work clarifies the RAMP-modulated CLR ligand selectivity mechanism and provides AM and CGRP variants that are valuable pharmacological tools and may have potential as long-acting therapeutics.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,Receptor activity-modifying protein 2,Calcitonin gene-related peptide type 1 receptor591Escherichia coli K-12Homo sapiensMutation(s): 1 
Gene Names: malEb4034JW3994RAMP2CALCRLCGRPR
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for O60895 (Homo sapiens)
Explore O60895 
Go to UniProtKB:  O60895
PHAROS:  O60895
GTEx:  ENSG00000131477 
Find proteins for Q16602 (Homo sapiens)
Explore Q16602 
Go to UniProtKB:  Q16602
PHAROS:  Q16602
GTEx:  ENSG00000064989 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9O60895Q16602
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ADM16Homo sapiensMutation(s): 4 
UniProt & NIH Common Fund Data Resources
Find proteins for P35318 (Homo sapiens)
Explore P35318 
Go to UniProtKB:  P35318
PHAROS:  P35318
GTEx:  ENSG00000148926 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35318
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChains NameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
C
alpha-maltoseOligosaccharide / Nutrient
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.017α = 90
b = 84.993β = 90
c = 123.064γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM104251
American Heart AssociationUnited States18PRE33990152

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description