8F2B | pdb_00008f2b

Amylin 3 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

Validation slider image for 8F2B

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 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.

Macromolecule Content 

  • Total Structure Weight: 191.39 kDa 
  • Atom Count: 10,360 
  • Modeled Residue Count: 1,274 
  • Deposited Residue Count: 1,641 
  • Unique protein chains: 7

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short394Homo 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)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63092
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1350Homo 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
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UniProt GroupP62873
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Homo 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: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
nanobody 35D [auth N]138Lama glamaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor activity-modifying protein 3149Homo sapiensMutation(s): 0 
Gene Names: RAMP3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O60896 (Homo sapiens)
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PHAROS:  O60896
GTEx:  ENSG00000122679 
Entity Groups
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UniProt GroupO60896
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
pramlintide analogue San45F [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 
Entity Groups
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UniProt GroupP10997
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Calcitonin receptorG [auth R]501Homo sapiensMutation(s): 0 
Gene Names: CALCR
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P30988 (Homo sapiens)
Explore P30988 
Go to UniProtKB:  P30988
PHAROS:  P30988
GTEx:  ENSG00000004948 
Entity Groups
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UniProt GroupP30988
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P30988-2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P42

Query on P42



Download:Ideal Coordinates CCD File
T [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
Y01

Query on Y01



Download:Ideal Coordinates CCD File
U [auth R],
V [auth R]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
D6M
(Subject of Investigation/LOI)

Query on D6M



Download:Ideal Coordinates CCD File
H [auth P]N-hexadecanoyl-L-glutamic acid
C21 H39 N O5
KMAOMYOPEIRFLB-SFHVURJKSA-N
PLM

Query on PLM



Download:Ideal Coordinates CCD File
L [auth R]
M [auth R]
N [auth R]
O [auth R]
P [auth R]
L [auth R],
M [auth R],
N [auth R],
O [auth R],
P [auth R],
Q [auth R],
R,
S [auth R]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
I [auth R],
J [auth R],
K [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: 2024-10-23
    Changes: Data collection, Structure summary