9PVP | pdb_00009pvp

Cryo-EM structure of receptor tyrosine kinase ROS1 extracellular domain

  • Classification: TRANSFERASE
  • Organism(s): Mus musculus
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-08-03 Released: 2026-02-25 
  • Deposition Author(s): Li, H., Klein, D.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9PVP

This is version 1.2 of the entry. See complete history

Literature

Clustering and a conformational switch drive activation of the mammalian receptor tyrosine kinase ROS1.

Li, H.Zhang, J.Li, T.Wang, Y.Alarcon, C.R.Klein, D.E.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-69630-7
  • Primary Citation Related Structures: 
    10FT, 10GH, 9DZ4, 9PVP, 9PWQ

  • PubMed Abstract: 

    Receptor tyrosine kinases (RTKs) are key regulators of cellular signaling and are often co-opted in cancer. ROS1 is an orphan RTK aberrantly expressed in multiple tumors, yet no approved biologic therapies target it, and its activation mechanism remains unknown. Here, we present Cryo-EM structures of mammalian ROS1 in ligand-free and NELL2-bound states, revealing how trimeric NELL2 induces both receptor clustering and a conformational switch that relieves receptor autoinhibition - both mechanisms are required for ROS1 activation. These structures, along with biochemical characterization, reflect a striking evolutionary divergence in regulatory logic compared to the invertebrate ortholog Sevenless (dROS1), highlighting how conserved RTKs can adopt fundamentally different activation strategies. Guided by these structural insights, we develop monoclonal antibodies that either block ligand binding or trap ROS1 in an inactive conformation. These agents potently suppress ROS1 signaling, representing distinct mechanistic classes of biologics that directly target ROS1 activity. Our findings elucidate a distinct mode of RTK regulation and establish a therapeutic framework for cancers driven by ROS1.


  • Organizational Affiliation
    • Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.

Macromolecule Content 

  • Total Structure Weight: 210.19 kDa 
  • Atom Count: 13,753 
  • Modeled Residue Count: 1,715 
  • Deposited Residue Count: 1,854 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase ROS1,854Mus musculusMutation(s): 0 
Gene Names: Ros1RosRos-1
EC: 2.7.10.1
UniProt
Find proteins for Q78DX7 (Mus musculus)
Explore Q78DX7 
Go to UniProtKB:  Q78DX7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ78DX7
Glycosylation
Glycosylation Sites: 6Go to GlyGen: Q78DX7-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-25
    Type: Initial release
  • Version 1.1: 2026-03-04
    Changes: Data collection, Database references
  • Version 1.2: 2026-05-06
    Changes: Data collection, Database references