8EWY | pdb_00008ewy

Structure of Janus Kinase (JAK) dimer complexed with cytokine receptor intracellular domain

• PDB DOI: https://doi.org/10.2210/pdb8EWY/pdb
• EM Map EMD-28649: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2022-10-24 Released: 2023-03-08 
• Deposition Author(s): Caveney, N.A., Saxton, R.A., Waghray, D., Garcia, K.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of Janus kinase trans-activation.

Caveney, N.A., Saxton, R.A., Waghray, D., Glassman, C.R., Tsutsumi, N., Hubbard, S.R., Garcia, K.C.

(2023) Cell Rep 42: 112201-112201

• PubMed: 36867534 
• DOI: https://doi.org/10.1016/j.celrep.2023.112201
• Primary Citation Related Structures: 
  8EWY


• PubMed Abstract: 
  

  Janus kinases (JAKs) mediate signal transduction downstream of cytokine receptors. Cytokine-dependent dimerization is conveyed across the cell membrane to drive JAK dimerization, trans-phosphorylation, and activation. Activated JAKs in turn phosphorylate receptor intracellular domains (ICDs), resulting in the recruitment, phosphorylation, and activation of signal transducer and activator of transcription (STAT)-family transcription factors. The structural arrangement of a JAK1 dimer complex with IFNλR1 ICD was recently elucidated while bound by stabilizing nanobodies. While this revealed insights into the dimerization-dependent activation of JAKs and the role of oncogenic mutations in this process, the tyrosine kinase (TK) domains were separated by a distance not compatible with the trans-phosphorylation events between the TK domains. Here, we report the cryoelectron microscopy structure of a mouse JAK1 complex in a putative trans-activation state and expand these insights to other physiologically relevant JAK complexes, providing mechanistic insight into the crucial trans-activation step of JAK signaling and allosteric mechanisms of JAK inhibition.

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Organizational Affiliation: 
• Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 293.23 kDa 
• Atom Count: 10,844 
• Modeled Residue Count: 2,172 
• Deposited Residue Count: 2,516 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase	A, B	1,173	Mus musculus	Mutation(s): 1  Gene Names: Jak1 EC: 2.7.10.2
UniProt
Find proteins for P52332 (Mus musculus) Explore P52332  Go to UniProtKB:  P52332

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon lambda receptor 1	C, D	85	Mus musculus	Mutation(s): 0  Gene Names: Ifnlr1, Il28ra
UniProt & NIH Common Fund Data Resources
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P03069  Go to UniProtKB:  P03069
Find proteins for Q8CGK5 (Mus musculus) Explore Q8CGK5  Go to UniProtKB:  Q8CGK5
IMPC:  MGI:2429859
UniProt Groups	Q8CGK5P03069

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	F [auth A], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ADN	E [auth A], G [auth B]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-08 
Deposition Author(s): Caveney, N.A., Saxton, R.A., Waghray, D., Garcia, K.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37AI51321

Revision History  

• Version 1.0: 2023-03-08
  Type: Initial release
  
• Version 1.1: 2023-03-22
  Changes: Database references
• Version 1.2: 2024-12-25
  Changes: Advisory, Data collection, Derived calculations, Structure summary