6FEK | pdb_00006fek

Oncogenic point mutation of RET receptor tyrosine kinase

• PDB DOI: https://doi.org/10.2210/pdb6FEK/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2018-01-02 Released: 2018-02-28 
• Deposition Author(s): McDonald, N.Q., Kohno, T.
• Funding Organization(s): Francis Crick Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

A secondary RET mutation in the activation loop conferring resistance to vandetanib.

Nakaoku, T., Kohno, T., Araki, M., Niho, S., Chauhan, R., Knowles, P.P., Tsuchihara, K., Matsumoto, S., Shimada, Y., Mimaki, S., Ishii, G., Ichikawa, H., Nagatoishi, S., Tsumoto, K., Okuno, Y., Yoh, K., McDonald, N.Q., Goto, K.

(2018) Nat Commun 9: 625-625

• PubMed: 29434222 
• DOI: https://doi.org/10.1038/s41467-018-02994-7
• Primary Citation Related Structures: 
  6FEK


• PubMed Abstract: 
  

  Resistance to vandetanib, a type I RET kinase inhibitor, developed in a patient with metastatic lung adenocarcinoma harboring a CCDC6-RET fusion that initially exhibited a response to treatment. The resistant tumor acquired a secondary mutation resulting in a serine-to-phenylalanine substitution at codon 904 in the activation loop of the RET kinase domain. The S904F mutation confers resistance to vandetanib by increasing the ATP affinity and autophosphorylation activity of RET kinase. A reduced interaction with the drug is also observed in vitro for the S904F mutant by thermal shift assay. A crystal structure of the S904F mutant reveals a small hydrophobic core around F904 likely to enhance basal kinase activity by stabilizing an active conformer. Our findings indicate that missense mutations in the activation loop of the kinase domain are able to increase kinase activity and confer drug resistance through allosteric effects.

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Organizational Affiliation: 
• Division of Genome Biology, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 1040045, Japan.
Division of Genome Biology, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 1040045, Japan. [e-mail].
Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 1040045, Japan. [e-mail].
Advanced Institute for Computational Science, RIKEN, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe-city, Hyogo, 6500047, Japan.
Department of Clinical System Onco-Informatics, Graduate School of Medicine, Kyoto University, 54 Kawaracho, Shogoin, Kyoto-city, Kyoto, 6068507, Japan.
Department of Thoracic Oncology, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, Kashiwa-city, Chiba, 2778577, Japan.
Signaling and Structural Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 1040045, Japan.
Division of Pathology, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, 6-5-1, Kashiwanoha, Kashiwa-City, Chiba, 2778577, Japan.
Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shiroganedai, Minato-ku, Tokyo, 1088639, Japan.
Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.71 kDa 
• Atom Count: 2,343 
• Modeled Residue Count: 296 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase receptor Ret	A	299	Homo sapiens	Mutation(s): 1  Gene Names: RET, CDHF12, CDHR16, PTC, RET51 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07949 (Homo sapiens) Explore P07949  Go to UniProtKB:  P07949
PHAROS:  P07949 GTEx:  ENSG00000165731

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADN	E [auth A]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
FMT	B [auth A], C [auth A], D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.901	α = 90
b = 50.901	β = 90
c = 242.515	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): McDonald, N.Q., Kohno, T.

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Funding Organization	Location	Grant Number
Francis Crick Institute	United Kingdom	FC001115

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2018-05-02
  Changes: Data collection
• Version 1.2: 2024-10-16
  Changes: Advisory, Data collection, Database references, Structure summary