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- PDB-1yvj: Crystal structure of the Jak3 kinase domain in complex with a sta... -

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Basic information

Entry
Database: PDB / ID: 1yvj
TitleCrystal structure of the Jak3 kinase domain in complex with a staurosporine analogue
ComponentsTyrosine-protein kinase JAK3
KeywordsTRANSFERASE / TYROSINE KINASE / SCID / SEVERE COMBINED IMMUNODEFICIENCY / STAT5 / STAT6 / INTERLEUKIN-2 / COMMON-GAMMA CHAIN
Function / homology
Function and homology information


negative regulation of dendritic cell cytokine production / negative regulation of FasL production / response to interleukin-9 / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / negative regulation of T-helper 17 cell lineage commitment / interleukin-7-mediated signaling pathway / Interleukin-9 signaling ...negative regulation of dendritic cell cytokine production / negative regulation of FasL production / response to interleukin-9 / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / negative regulation of T-helper 17 cell lineage commitment / interleukin-7-mediated signaling pathway / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / negative regulation of T cell activation / regulation of T cell apoptotic process / interleukin-2-mediated signaling pathway / negative regulation of interleukin-12 production / tyrosine phosphorylation of STAT protein / interleukin-15-mediated signaling pathway / negative regulation of thymocyte apoptotic process / Interleukin-15 signaling / Interleukin-2 signaling / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / extrinsic component of plasma membrane / Signaling by ALK / Interleukin-20 family signaling / negative regulation of interleukin-10 production / enzyme-linked receptor protein signaling pathway / T cell homeostasis / extrinsic component of cytoplasmic side of plasma membrane / cell surface receptor signaling pathway via JAK-STAT / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / Interleukin-7 signaling / B cell differentiation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / cytoplasmic side of plasma membrane / RAF/MAP kinase cascade / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / protein phosphatase binding / regulation of apoptotic process / adaptive immune response / Potential therapeutics for SARS / cell differentiation / cytoskeleton / intracellular signal transduction / endosome / protein phosphorylation / innate immune response / ATP binding / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak3 / SH2 domain / 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 ...Tyrosine-protein kinase, non-receptor Jak3 / SH2 domain / 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 domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
1,2,3,4-TETRAHYDROGEN-STAUROSPORINE / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Tyrosine-protein kinase JAK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBoggon, T.J. / Li, Y. / Manley, P.W. / Eck, M.J.
CitationJournal: Blood / Year: 2005
Title: Crystal structure of the Jak3 kinase domain in complex with a staurosporine analog
Authors: Boggon, T.J. / Li, Y. / Manley, P.W. / Eck, M.J.
History
DepositionFeb 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase JAK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9824
Polymers33,2031
Non-polymers7793
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.307, 54.215, 118.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein kinase JAK3 / E.C.2.7.1.112 / Janus kinase 3 / JAK-3 / JAK3 / Leukocyte janus kinase / L-JAK


Mass: 33202.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAK3 / Production host: Escherichia coli (E. coli) / References: UniProt: P52333, EC: 2.7.1.112
#2: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-4ST / 1,2,3,4-TETRAHYDROGEN-STAUROSPORINE / AFN941


Mass: 470.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H30N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: malonate, glycerol, pipes, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 2004
RadiationMonochromator: Osmic confocal Max-Flux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→24.97 Å / Num. obs: 9949 / % possible obs: 97.9 % / Observed criterion σ(I): 9.2 / Redundancy: 3.1 % / Biso Wilson estimate: 56.4 Å2 / Rsym value: 0.11
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 3.1 % / Rsym value: 0.57 / % possible all: 97.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M17

1m17


Resolution: 2.55→24.97 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1132120.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 481 4.9 %RANDOM
Rwork0.204 ---
all0.2041 9913 --
obs0.2041 9913 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.058 Å2 / ksol: 0.364058 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.98 Å20 Å20 Å2
2---1.29 Å20 Å2
3----6.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.55→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 51 165 2575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.46
LS refinement shellResolution: 2.55→2.64 Å / Rfactor Rfree error: 0.072 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.471 43 5 %
Rwork0.332 812 -
obs--86.7 %

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