9PLO | pdb_00009plo

Structure of alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and N-(5-methylnaphthalen-1-yl)pyridin-4-amine (compound 4905)

• PDB DOI: https://doi.org/10.2210/pdb9PLO/pdb
• EM Map EMD-71719: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Trichoplusia ni, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-07-15 Released: 2025-07-30 
• Deposition Author(s): Srinivasan, K., Xu, X., Mailhot, O., Manglik, A., Shoichet, B.
• Funding Organization(s): Defense Advanced Research Projects Agency (DARPA)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Toward a Random Background for Ligand Optimization

Xu, X., Mailhot, O., Correy, G., Huang, X.P., Braz, J., Shi, D., Srinivasan, K., Holota, Y., Kuziv, Y., Tsoutsouvas, C., Levinzon, N., Doruk, Y.U., Rachman, M., Diolaiti, M., Stevens, M., Liu, F., Hubner, H., Wang, J., Wu, Y., Ashworth, A., Makriyannis, A., Zhang, Y., Moroz, Y., Gmeiner, P., Abel, R., Manglik, A., Basbaum, A., Roth, B., Fraser, J., Shoichet, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 169.04 kDa 
• Atom Count: 8,657 
• Modeled Residue Count: 1,110 
• Deposited Residue Count: 1,533 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(o) subunit alpha	A	354	Homo sapiens	Mutation(s): 0  Gene Names: GNAO1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P09471 (Homo sapiens) Explore P09471  Go to UniProtKB:  P09471
PHAROS:  P09471 GTEx:  ENSG00000087258

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	358	Homo sapiens	Mutation(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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-2A adrenergic receptor	D [auth R]	491	Homo sapiens	Mutation(s): 0  Gene Names: ADRA2A, ADRA2R, ADRAR
UniProt & NIH Common Fund Data Resources
Find proteins for P08913 (Homo sapiens) Explore P08913  Go to UniProtKB:  P08913
PHAROS:  P08913 GTEx:  ENSG00000150594

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	E [auth S]	259	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CIU (Subject of Investigation/LOI)	F [auth R]	N-(5-methylnaphthalen-1-yl)pyridin-4-amine C16 H14 N2 WUHPUCOIAGCLKE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Srinivasan, K., Xu, X., Mailhot, O., Manglik, A., Shoichet, B.

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Funding Organization	Location	Grant Number
Defense Advanced Research Projects Agency (DARPA)	United States	--

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release