8F0J

Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural insight into selectivity of amylin and calcitonin receptor agonists.

Cao, J.Belousoff, M.J.Gerrard, E.Danev, R.Fletcher, M.M.Dal Maso, E.Schreuder, H.Lorenz, K.Evers, A.Tiwari, G.Besenius, M.Li, Z.Johnson, R.M.Wootten, D.Sexton, P.M.

(2024) Nat Chem Biol 20: 162-169

  • DOI: https://doi.org/10.1038/s41589-023-01393-4
  • Primary Citation of Related Structures:  
    8F0J, 8F0K, 8F2A, 8F2B

  • PubMed Abstract: 

    Amylin receptors (AMYRs), heterodimers of the calcitonin receptor (CTR) and one of three receptor activity-modifying proteins, are promising obesity targets. A hallmark of AMYR activation by Amy is the formation of a 'bypass' secondary structural motif (residues S19-P25). This study explored potential tuning of peptide selectivity through modification to residues 19-22, resulting in a selective AMYR agonist, San385, as well as nonselective dual amylin and calcitonin receptor agonists (DACRAs), with San45 being an exemplar. We determined the structure and dynamics of San385-bound AMY 3 R, and San45 bound to AMY 3 R or CTR. San45, via its conjugated lipid at position 21, was anchored at the edge of the receptor bundle, enabling a stable, alternative binding mode when bound to the CTR, in addition to the bypass mode of binding to AMY 3 R. Targeted lipid modification may provide a single intervention strategy for design of long-acting, nonselective, Amy-based DACRAs with potential anti-obesity effects.


  • Organizational Affiliation

    Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
pramlintide analogue San45A [auth P]38Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P10997 (Homo sapiens)
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Go to UniProtKB:  P10997
PHAROS:  P10997
GTEx:  ENSG00000121351 
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UniProt GroupP10997
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calcitonin receptorB [auth R]501Homo sapiensMutation(s): 0 
Gene Names: CALCR
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P30988 (Homo sapiens)
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PHAROS:  P30988
GTEx:  ENSG00000004948 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30988
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P30988-2
Sequence Annotations
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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
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
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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]350Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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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]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody 35F [auth N]138Lama glamaMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P42
Query on P42

Download Ideal Coordinates CCD File 
P [auth R](2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl]oxy}propyl 2-(trimethylammonio)ethyl phosphate
C42 H88 N O8 P
LYKCEYRWVRQPBD-FEWNNGCESA-N
PTY
Query on PTY

Download Ideal Coordinates CCD File 
J [auth R],
K [auth R],
O [auth R]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
Y01
Query on Y01

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M [auth R],
N [auth R]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
D6M (Subject of Investigation/LOI)
Query on D6M

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G [auth P]N-hexadecanoyl-L-glutamic acid
C21 H39 N O5
KMAOMYOPEIRFLB-SFHVURJKSA-N
PLM
Query on PLM

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L [auth R]
Q [auth R]
R
S [auth R]
T [auth R]
L [auth R],
Q [auth R],
R,
S [auth R],
T [auth R],
U [auth R],
V [auth R],
W [auth R]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth R],
I [auth R]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 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
Australian Research Council (ARC)AustraliaIC200100052
National Health and Medical Research Council (NHMRC, Australia)Australia1120919
National Health and Medical Research Council (NHMRC, Australia)Australia1159006
National Health and Medical Research Council (NHMRC, Australia)Australia1150083
National Health and Medical Research Council (NHMRC, Australia)Australia1154434
National Health and Medical Research Council (NHMRC, Australia)Australia1155302
Japan Science and TechnologyJapan18069571
Takeda Science FoundationJapan2019 Medical Research Grant

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-02-14
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Source and taxonomy
  • Version 1.4: 2024-10-30
    Changes: Data collection, Structure summary