9P9U | pdb_00009p9u

EGFR-KDD with compound2

  • Classification: ONCOPROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Insect BA phytoplasma
  • Mutation(s): No 

  • Deposited: 2025-06-24 Released: 2025-11-19 
  • Deposition Author(s): Han, L., Petrova, Z.O., Lemmon, M.A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9P9U

This is version 1.2 of the entry. See complete history

Literature

The role of kinase domain dimerization in EGFR activation.

Petrova, Z.O.Han, L.Tsutsui, Y.Sheetz, J.B.Ashtekar, K.D.Lemmon, M.A.

(2026) Structure 34: 426-440.e6

  • DOI: https://doi.org/10.1016/j.str.2025.11.017
  • Primary Citation Related Structures: 
    9P9U

  • PubMed Abstract: 

    The epidermal growth factor receptor (EGFR) was among the first receptor tyrosine kinases (RTKs) shown to be activated by ligand-induced dimerization. Structural studies explain how ligand binding induces the dimerization of EGFR's extracellular region. Unlike other RTKs, EGFR's intracellular tyrosine kinase domain (TKD) is activated allosterically in an asymmetric dimer that is observed crystallographically, but not in cryo-EM studies of intact EGFR. Here, we show that this asymmetric TKD dimer forms only transiently - explaining its lack of definition by cryo-EM. By engineering an asymmetric TKD dimer and studying a TKD-duplicated lung cancer EGFR variant, we show that TKD dimerization increases kinase activity by several hundred-fold. We were also able to stabilize and visualize discrete asymmetric EGFR TKD dimers at high resolution using cryo-EM. Our findings argue that oncogenic mutations activate EGFR primarily by promoting TKD dimerization, and suggest that the transient nature of EGFR TKD dimers may allow biased EGFR signaling.


  • Organizational Affiliation
    • Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA.

Macromolecule Content 

  • Total Structure Weight: 77.88 kDa 
  • Atom Count: 4,407 
  • Modeled Residue Count: 545 
  • Deposited Residue Count: 678 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor678Homo sapiensMutation(s): 0 
Gene Names: EGFRERBBERBB1HER1
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
PHAROS:  P00533
GTEx:  ENSG00000146648 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6JS
(Subject of Investigation/LOI)

Query on 6JS



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
3-(furan-2-yl)-N-[5-(furan-2-yl)-2-methoxyphenyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C20 H15 N5 O3
ZKGQOANFVSVQMS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.3

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM122485
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01-CA198164
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesP50-DE030707

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2026-06-03
    Changes: Data collection, Database references