9MNI | pdb_00009mni

CGRP Receptor in complex with dC2_050

• PDB DOI: https://doi.org/10.2210/pdb9MNI/pdb
• EM Map EMD-48424: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-21 Released: 2025-10-22 
• Deposition Author(s): Cao, J., Cary, B.P., Belousoff, M.J., Wootten, D.L.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

De novo design of miniprotein agonists and antagonists targeting G protein-coupled receptors.

Muratspahic, E., Feldman, D., Kim, D.E., Qu, X., Bratovianu, A.M., Rivera-Sanchez, P., Dimitri, F., Cao, J., Cary, B.P., Belousoff, M.J., Keov, P., Chen, Q., Ren, Y., Fine, J., Sappington, I., Schlichthaerle, T., Zhang, J.Z., Pillai, A., Mihaljevic, L., Bauer, M., Torres, S.V., Motmaen, A., Lee, G.R., Tran, L., Wang, X., Goreshnik, I., Vafeados, D.K., Svendsen, J.E., Hosseinzadeh, P., Lindegaard, N., Brandt, M., Waltenspuhl, Y., Deibler, K., Oostdyk, L., Cao, W., Anantharaman, L., Stewart, L., Halloran, L., Spangler, J.B., Sexton, P.M., Roth, B.L., Krumm, B.E., Wootten, D., Tate, C.G., Norn, C., Baker, D.

(2025) bioRxiv 

• PubMed: 40501737 
• DOI: https://doi.org/10.1101/2025.03.23.644666
• Primary Citation of Related Structures:  
  9MNI


• PubMed Abstract: 
  

  G protein-coupled receptors (GPCRs) play key roles in physiology and are central targets for drug discovery and development, yet the design of protein agonists and antagonists has been challenging as GPCRs are integral membrane proteins and conformationally dynamic. Here we describe computational de novo design methods and a high throughput "receptor diversion" microscopy-based screen for generating GPCR binding miniproteins with high affinity, potency and selectivity, and the use of these methods to generate MRGPRX1 agonists and CXCR4, GLP1R, GIPR, GCGR and CGRPR antagonists. Cryo-electron microscopy data reveals atomic-level agreement between designed and experimentally determined structures for CGRPR-bound antagonists and MRGPRX1-bound agonists, confirming precise conformational control of receptor function. Our de novo design and screening approach opens new frontiers in GPCR drug discovery and development.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA 98195.
Institute for Protein Design, University of Washington, Seattle, WA 98195.
BioInnovation Institute, DK2200 Copenhagen N, Denmark.
Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195.
Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC Australia.
ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC Australia.
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21208, USA; Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD 21231, USA.
Department of Chemical Engineering, University of Washington, Seattle, WA 98195.
Department of Bioengineering, Knight Campus for Accelerating Scientific Impact, University of Oregon, 6231 University of Oregon, Eugene, OR, 97403, USA.
Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403, USA.
Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark.
LeadHunter Services, Eurofins DiscoverX, LLC, CA-94583, California, USA.
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD 21231, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA and NIMH Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 81.23 kDa 
• Atom Count: 3,604 
• Modeled Residue Count: 516 
• Deposited Residue Count: 708 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor activity-modifying protein 1	A [auth E]	149	Homo sapiens	Mutation(s): 0  Gene Names: RAMP1
UniProt & NIH Common Fund Data Resources
Find proteins for O60894 (Homo sapiens) Explore O60894  Go to UniProtKB:  O60894
PHAROS:  O60894 GTEx:  ENSG00000132329

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcitonin gene-related peptide type 1 receptor	B [auth R]	490	Homo sapiens	Mutation(s): 0  Gene Names: CALCRL, CGRPR
UniProt & NIH Common Fund Data Resources
Find proteins for Q16602 (Homo sapiens) Explore Q16602  Go to UniProtKB:  Q16602
PHAROS:  Q16602 GTEx:  ENSG00000064989

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed minibinder - dC2_050	C [auth A]	69	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419:
RECONSTRUCTION	cryoSPARC	4.6.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Cao, J., Cary, B.P., Belousoff, M.J., Wootten, D.L.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1150083
Australian Research Council (ARC)	Australia	DP210101504
National Health and Medical Research Council (NHMRC, Australia)	Australia	2026300
Australian Research Council (ARC)	Australia	IC200100052

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release