4L01 | pdb_00004l01

Crystal structure of the V658F apo Jak1 pseudokinase domain

• PDB DOI: https://doi.org/10.2210/pdb4L01/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2013-05-30 Released: 2013-09-04 
• Deposition Author(s): Toms, A.V., Rogers, J.M., Eck, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Structure of a pseudokinase-domain switch that controls oncogenic activation of Jak kinases.

Toms, A.V., Deshpande, A., McNally, R., Jeong, Y., Rogers, J.M., Kim, C.U., Gruner, S.M., Ficarro, S.B., Marto, J.A., Sattler, M., Griffin, J.D., Eck, M.J.

(2013) Nat Struct Mol Biol 20: 1221-1223

• PubMed: 24013208 
• DOI: https://doi.org/10.1038/nsmb.2673
• Primary Citation Related Structures: 
  4L00, 4L01


• PubMed Abstract: 
  

  The V617F mutation in the Jak2 pseudokinase domain causes myeloproliferative neoplasms, and the equivalent mutation in Jak1 (V658F) is found in T-cell leukemias. Crystal structures of wild-type and V658F-mutant human Jak1 pseudokinase reveal a conformational switch that remodels a linker segment encoded by exon 12, which is also a site of mutations in Jak2. This switch is required for V617F-mediated Jak2 activation and possibly for physiologic Jak activation.

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Organizational Affiliation: 
• 1] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA. [2] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.93 kDa 
• Atom Count: 4,700 
• Modeled Residue Count: 548 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK1	A, B	304	Homo sapiens	Mutation(s): 1  Gene Names: JAK1, JAK1A, JAK1B EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P23458 (Homo sapiens) Explore P23458  Go to UniProtKB:  P23458
PHAROS:  P23458 GTEx:  ENSG00000162434

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.288	α = 90
b = 80.557	β = 95.29
c = 76.555	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Toms, A.V., Rogers, J.M., Eck, M.J.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2013-10-02
  Changes: Database references
• Version 1.2: 2014-02-05
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references