9PLN | pdb_00009pln

Locally-refined 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/pdb9PLN/pdb
EM Map EMD-71718: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-07-15 Released: 2025-08-20
Deposition Author(s): Srinivasan, K., Xu, X., Mailhot, O., Manglik, A., Shoichet, B.
Funding Organization(s): Defense Advanced Research Projects Agency (DARPA)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 53.88 kDa
Atom Count: 2,121
Modeled Residue Count: 266
Deposited Residue Count: 491
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-2A adrenergic receptor	A [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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08913
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CIU (Subject of Investigation/LOI) Query on A1CIU Download Ideal Coordinates CCD File SDF format, chain B [auth R] MOL2 format, chain B [auth R] mmCIF format, chain B [auth R]	B [auth R]	N-(5-methylnaphthalen-1-yl)pyridin-4-amine C₁₆ H₁₄ N₂ WUHPUCOIAGCLKE-UHFFFAOYSA-N		Interactions Focus chain B [auth R] Interactions & Density Focus chain B [auth R]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-20

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-08-20
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.