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- PDB-4l00: Crystal structure of the apo Jak1 pseudokinase domain -

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Basic information

Entry
Database: PDB / ID: 4l00
TitleCrystal structure of the apo Jak1 pseudokinase domain
ComponentsTyrosine-protein kinase JAK1
KeywordsTRANSFERASE / kinase domain fold / regulatory
Function / homology
Function and homology information


protein localization to cell-cell junction / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / T-helper 17 cell lineage commitment / positive regulation of homotypic cell-cell adhesion / type III interferon-mediated signaling pathway / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway ...protein localization to cell-cell junction / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / T-helper 17 cell lineage commitment / positive regulation of homotypic cell-cell adhesion / type III interferon-mediated signaling pathway / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / Interleukin-12 signaling / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-2 signaling / growth hormone receptor binding / Other interleukin signaling / IFNG signaling activates MAPKs / Interleukin-20 family signaling / Interleukin-6 signaling / type I interferon-mediated signaling pathway / interleukin-6-mediated signaling pathway / positive regulation of sprouting angiogenesis / MAPK3 (ERK1) activation / Interleukin-10 signaling / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / Signaling by CSF3 (G-CSF) / extrinsic component of cytoplasmic side of plasma membrane / Interleukin-7 signaling / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / ISG15 antiviral mechanism / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / Interferon gamma signaling / Interferon alpha/beta signaling / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / cell differentiation / cytoskeleton / endosome / intracellular signal transduction / protein phosphorylation / response to antibiotic / focal adhesion / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak1 / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / FERM central domain / FERM superfamily, second domain ...Tyrosine-protein kinase, non-receptor Jak1 / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase JAK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsToms, A.V. / Eck, M.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure of a pseudokinase-domain switch that controls oncogenic activation of Jak kinases.
Authors: 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.
History
DepositionMay 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase JAK1
B: Tyrosine-protein kinase JAK1


Theoretical massNumber of molelcules
Total (without water)69,8362
Polymers69,8362
Non-polymers00
Water6,774376
1
A: Tyrosine-protein kinase JAK1


Theoretical massNumber of molelcules
Total (without water)34,9181
Polymers34,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase JAK1


Theoretical massNumber of molelcules
Total (without water)34,9181
Polymers34,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-13 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.026, 80.656, 76.231
Angle α, β, γ (deg.)90.00, 95.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein kinase JAK1 / Janus kinase 1 / JAK-1


Mass: 34918.117 Da / Num. of mol.: 2 / Fragment: pseudokinase domain (UNP residues 561-860)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAK1, JAK1A, JAK1B
References: UniProt: P23458, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9772 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 48311 / % possible obs: 97.38 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.846 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20302 2527 5 %RANDOM
Rwork0.16877 ---
obs0.17052 48311 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.103 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0 Å2-0.2 Å2
2---0.02 Å2-0 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4481 0 0 376 4857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194668
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9766328
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1675582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87323.75208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15115886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9191534
X-RAY DIFFRACTIONr_chiral_restr0.1060.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213470
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 182 -
Rwork0.219 3310 -
obs--91.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8850.6147-0.18080.7423-0.12793.4451-0.0620.16240.4138-0.01360.0533-0.03360.13280.2580.00870.09130.0053-0.02170.04290.03180.16799.20242.70448.382
22.60180.1575-0.06842.155-0.07641.4015-0.06580.04820.30820.08050.0292-0.0115-0.12550.10340.03650.0418-0.0237-0.02640.03010.03330.08675.90639.65850.647
32.02030.98120.2682.18150.0971.4276-0.21570.40680.0406-0.31450.1969-0.08350.01350.11250.01890.083-0.04740.01870.10880.03040.03643.0129.4740.822
42.15650.1836-0.03731.6583-0.01491.2735-0.05950.1187-0.0071-0.09080.0559-0.11980.10710.02860.00360.0537-0.0192-0.0010.02460.00740.03540.27528.0847.869
52.4723-0.1619-0.10191.77470.261.0785-0.04510.16590.1632-0.01590.00490.15090.0215-0.13750.04020.0401-0.02110.00040.04630.01940.0611-13.32429.53448.811
61.88980.14710.56912.0024-0.72081.5032-0.03020.1393-0.1796-0.0410.06820.0170.1741-0.0324-0.0380.0626-0.02280.01590.0524-0.010.0624-12.85118.18651.665
71.12470.0405-0.12823.54033.30873.21780.01460.05120.1459-0.2531-0.19770.2379-0.1662-0.16720.18310.15890.0063-0.01340.08740.02230.0817-0.75253.12873.471
81.95720.3258-1.09381.57830.31483.33340.05530.06350.1066-0.2151-0.05560.0856-0.1137-0.06340.00020.04120.00320.01350.0404-0.01460.08223.18848.66774.31
92.4721-0.87250.12652.15010.04152.15-0.0847-0.31030.16740.26630.18380.0267-0.1467-0.0422-0.09910.08850.00410.04720.0664-0.05690.0915.97946.46887.736
102.22890.0155-0.92381.7025-0.30162.9417-0.0065-0.16930.05160.18630.11520.03030.01780.0025-0.10870.05360.017200.0273-0.01810.06738.87940.8783.619
113.8458-0.028-0.07691.6353-0.33432.8977-0.1063-0.25450.3040.08850.0426-0.2988-0.03040.36150.06370.03670.0193-0.01750.0787-0.0480.147622.36541.08482.09
124.16811.8366-0.78414.3252-0.62792.8882-0.0853-0.4924-0.09140.49480.0498-0.24540.37020.35380.03560.16930.1166-0.00720.1327-0.00460.124122.57430.64487.06
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A564 - 604
2X-RAY DIFFRACTION2A615 - 650
3X-RAY DIFFRACTION3A651 - 700
4X-RAY DIFFRACTION4A701 - 750
5X-RAY DIFFRACTION5A751 - 800
6X-RAY DIFFRACTION6A801 - 850
7X-RAY DIFFRACTION7B565 - 605
8X-RAY DIFFRACTION8B614 - 650
9X-RAY DIFFRACTION9B651 - 700
10X-RAY DIFFRACTION10B701 - 750
11X-RAY DIFFRACTION11B751 - 800
12X-RAY DIFFRACTION12B801 - 850

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