9W3F | pdb_00009w3f

Cryo-EM structure of the human beta2-adrenergic receptor in complex with a novel antagonist

• PDB DOI: https://doi.org/10.2210/pdb9W3F/pdb
• EM Map EMD-65599: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Tequatrovirus T4, Lama glama
• Expression System: Spodoptera, Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-07-29 Released: 2026-06-10 
• Deposition Author(s): Xu, T., Liu, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A negative survival pressure selection system enables GPCR antagonist screening.

Xu, T., Sun, Q., Zhang, S., Liu, T., Sun, X., Wang, X., Lin, B., Liu, Z., Wang, J., He, G., Liu, X.

(2026) Cell Discov 12

• PubMed: 42129146 
• DOI: https://doi.org/10.1038/s41421-026-00892-7
• Primary Citation Related Structures: 
  9W3F

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Organizational Affiliation: 
• State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.
Memoo (Beijing) Technology Co. Ltd., Beijing, China.
School of Basic Medical Sciences, Tsinghua University, Beijing, China.
School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen, Guangdong, China.
School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, China.
Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China.
Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning, China.
Department of Anesthesiology, Shenzhen Children's Hospital, Shenzhen, Guangdong, China. [e-mail].
Memoo (Beijing) Technology Co. Ltd., Beijing, China. [e-mail].
College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China. [e-mail].
State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China. [e-mail].
Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China. [e-mail].
State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China. [e-mail].
Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China. [e-mail].
Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 72.4 kDa 
• Atom Count: 2,993 
• Modeled Residue Count: 393 
• Deposited Residue Count: 642 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2 adrenergic receptor,Endolysin	A	517	Homo sapiens, Tequatrovirus T4	Mutation(s): 0  Gene Names: ADRB2, ADRB2R, B2AR, E EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
Find proteins for P07550 (Homo sapiens) Explore P07550  Go to UniProtKB:  P07550
PHAROS:  P07550 GTEx:  ENSG00000169252
UniProt Groups	P07550P00720

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta2 adrenogic receptor inactive-state stabling nanobody Nb60	B	125	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BER (Subject of Investigation/LOI)	C [auth A]	BERBERINE C20 H18 N O4 YBHILYKTIRIUTE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-10 
Deposition Author(s): Xu, T., Liu, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-06-10
  Type: Initial release