9BFQ | pdb_00009bfq

Cryo-EM structure of Sevenless in complex with Bride of Sevenless

• PDB DOI: https://doi.org/10.2210/pdb9BFQ/pdb
• EM Map EMD-44503: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Drosophila melanogaster, Homo sapiens
• Mutation(s): No 


• Deposited: 2024-04-18 Released: 2025-01-29 
• Deposition Author(s): Cerutti, G., Shapiro, L.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.09 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures and pH-dependent dimerization of the sevenless receptor tyrosine kinase.

Cerutti, G., Arias, R., Bahna, F., Mannepalli, S., Katsamba, P.S., Ahlsen, G., Kloss, B., Bruni, R., Tomlinson, A., Shapiro, L.

(2024) Mol Cell 84: 4677-4690.e6

• PubMed: 39510067 
• DOI: https://doi.org/10.1016/j.molcel.2024.10.017
• Primary Citation Related Structures: 
  9BFP, 9BFQ, 9BFR, 9BFS, 9BFU


• PubMed Abstract: 
  

  Sevenless (Sev) is a Drosophila receptor tyrosine kinase (RTK) required for the specification of the R7 photoreceptor. It is cleaved into α and β subunits and binds the ectodomain of the G-protein-coupled receptor bride of sevenless (Boss). Previous work showed that the Boss ectodomain could bind but not activate Sev; rather, the whole seven-pass transmembrane Boss was required. Here, we show that Sev does not need to be cleaved to function and that a single-pass transmembrane form of Boss activates Sev. We use cryo-electron microscopy and biophysical methods to determine the structural basis of ligand binding and pH-dependent dimerization of Sev, and we discuss the implications in the process of Sev activation. The Sev human homolog, receptor oncogene from sarcoma 1 (ROS1), is associated with oncogenic transformations, and we discuss their structural similarities.

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Organizational Affiliation: 
• Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.
Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Genetics and Development, Columbia University, New York, NY 10027, USA.
Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
New York Structural Biology Center, New York, NY 10027, USA.
Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Genetics and Development, Columbia University, New York, NY 10027, USA. Electronic address: [e-mail].
Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 283.68 kDa 
• Atom Count: 10,958 
• Modeled Residue Count: 1,365 
• Deposited Residue Count: 2,507 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein sevenless	A	2,002	Drosophila melanogaster	Mutation(s): 0  Gene Names: sev, HD-265, CG18085 EC: 2.7.10.1
UniProt
Find proteins for P13368 (Drosophila melanogaster) Explore P13368  Go to UniProtKB:  P13368
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P13368-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein bride of sevenless	B	505	Drosophila melanogaster	Mutation(s): 0  Gene Names: boss, CG8285
UniProt
Find proteins for P22815 (Drosophila melanogaster) Explore P22815  Go to UniProtKB:  P22815
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P22815-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.09 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Cerutti, G., Shapiro, L.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Data collection