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- PDB-4fvp: Crystal structure of the Jak2 pseudokinase domain (apo form) -

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Basic information

Entry
Database: PDB / ID: 4fvp
TitleCrystal structure of the Jak2 pseudokinase domain (apo form)
ComponentsTyrosine-protein kinase JAK2
KeywordsTRANSFERASE / JANUS PROTEIN KINASE / PSEUDOKINASE / ATP BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


interleukin-35-mediated signaling pathway / nuclear receptor-mediated mineralocorticoid signaling pathway / histone H3Y41 kinase activity / symbiont-induced defense-related programmed cell death / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / mammary gland epithelium development / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway ...interleukin-35-mediated signaling pathway / nuclear receptor-mediated mineralocorticoid signaling pathway / histone H3Y41 kinase activity / symbiont-induced defense-related programmed cell death / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / mammary gland epithelium development / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / thrombopoietin-mediated signaling pathway / Signaling by Erythropoietin / collagen-activated signaling pathway / interleukin-12 receptor binding / Erythropoietin activates STAT5 / interleukin-5-mediated signaling pathway / activation of Janus kinase activity / response to interleukin-12 / Erythropoietin activates Phospholipase C gamma (PLCG) / positive regulation of leukocyte proliferation / type 1 angiotensin receptor binding / post-embryonic hemopoiesis / interleukin-12 receptor complex / erythropoietin-mediated signaling pathway / interleukin-23 receptor complex / interleukin-23-mediated signaling pathway / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / interleukin-12-mediated signaling pathway / positive regulation of MHC class II biosynthetic process / positive regulation of NK T cell proliferation / acetylcholine receptor binding / positive regulation of platelet activation / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway / positive regulation of platelet aggregation / Signaling by Leptin / Interleukin-12 signaling / positive regulation of epithelial cell apoptotic process / IL-6-type cytokine receptor ligand interactions / Interleukin-27 signaling / Interleukin-35 Signalling / regulation of nitric oxide biosynthetic process / growth hormone receptor binding / positive regulation of cell-substrate adhesion / axon regeneration / response to hydroperoxide / extrinsic component of cytoplasmic side of plasma membrane / regulation of receptor signaling pathway via JAK-STAT / negative regulation of cardiac muscle cell apoptotic process / growth hormone receptor signaling pathway / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of cell-cell adhesion / extrinsic component of plasma membrane / Interleukin-20 family signaling / IFNG signaling activates MAPKs / Interleukin-6 signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / peptide hormone receptor binding / enzyme-linked receptor protein signaling pathway / interleukin-6-mediated signaling pathway / MAPK3 (ERK1) activation / response to amine / Prolactin receptor signaling / MAPK1 (ERK2) activation / platelet-derived growth factor receptor signaling pathway / mesoderm development / positive regulation of natural killer cell proliferation / positive regulation of interleukin-17 production / response to tumor necrosis factor / signaling receptor activator activity / Interleukin-3, Interleukin-5 and GM-CSF signaling / positive regulation of SMAD protein signal transduction / insulin receptor substrate binding / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / cell surface receptor signaling pathway via JAK-STAT / cellular response to dexamethasone stimulus / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / Growth hormone receptor signaling / Erythropoietin activates RAS / phosphatidylinositol 3-kinase binding / Signaling by CSF3 (G-CSF) / positive regulation of vascular associated smooth muscle cell proliferation / extrinsic apoptotic signaling pathway / actin filament polymerization / positive regulation of T cell proliferation / negative regulation of cytokine production involved in inflammatory response / SH2 domain binding / post-translational protein modification / lipopolysaccharide-mediated signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of interleukin-1 beta production / endosome lumen / positive regulation of apoptotic signaling pathway / erythrocyte differentiation / tumor necrosis factor-mediated signaling pathway / non-membrane spanning protein tyrosine kinase activity
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak2 / Janus kinase 2, pseudokinase domain / Janus kinase 2, catalytic domain / Tyrosine-protein kinase JAK2, SH2 domain / JAK2, FERM domain C-lobe / 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 / : ...Tyrosine-protein kinase, non-receptor Jak2 / Janus kinase 2, pseudokinase domain / Janus kinase 2, catalytic domain / Tyrosine-protein kinase JAK2, SH2 domain / JAK2, FERM domain C-lobe / 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 / SH2 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. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 JAK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsBandaranayake, R.M. / Hubbard, S.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Crystal structures of the JAK2 pseudokinase domain and the pathogenic mutant V617F.
Authors: Bandaranayake, R.M. / Ungureanu, D. / Shan, Y. / Shaw, D.E. / Silvennoinen, O. / Hubbard, S.R.
History
DepositionJun 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Aug 22, 2012Group: Database references
Revision 1.3Sep 13, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3053
Polymers33,1211
Non-polymers1842
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.362, 57.143, 60.996
Angle α, β, γ (deg.)90.00, 110.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein kinase JAK2 / Janus kinase 2 / JAK-2


Mass: 33120.961 Da / Num. of mol.: 1 / Fragment: Jak2 pseudokinase domain, UNP residues 536-812 / Mutation: W659A, W777A, F794H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAK2 / Plasmid: pFastBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O60674, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris/HCl, PEG 4000, pH 8.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 27, 2011 / Details: Osmic Blue
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 19131 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.039 / Χ2: 1.247 / Net I/σ(I): 23.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.01-2.083.50.12118571.309198.6
2.08-2.173.60.09619041.285199.9
2.17-2.263.60.0819241.251199.9
2.26-2.383.60.07218921.116199.9
2.38-2.533.70.06219051.032199.9
2.53-2.733.70.05519041.125199.8
2.73-33.70.04619301.1891100
3-3.443.70.03719201.3461100
3.44-4.333.80.0319211.535199.8
4.33-503.70.02719741.269199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
d*TREKdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M14

1m14


Resolution: 2.01→33.6 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2268 / WRfactor Rwork: 0.1931 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8723 / SU B: 6.646 / SU ML: 0.097 / SU R Cruickshank DPI: 0.1876 / SU Rfree: 0.1553 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 981 5.1 %RANDOM
Rwork0.1796 ---
obs0.1813 19090 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.16 Å2 / Biso mean: 25.6472 Å2 / Biso min: 12.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20.02 Å2
2---0.48 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.01→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 12 154 2306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022198
X-RAY DIFFRACTIONr_bond_other_d0.0060.021459
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9642983
X-RAY DIFFRACTIONr_angle_other_deg0.79933582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8565273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58325.248101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1915367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.222158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
LS refinement shellResolution: 2.011→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 79 -
Rwork0.201 1261 -
all-1340 -
obs--97.81 %
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)
18.424-0.2761-3.58045.42240.19947.12210.0258-0.06420.4238-0.03830.0253-0.3704-0.44190.4236-0.0510.1093-0.043-0.02730.0609-0.00980.06430.36527.95526.31
212.9081-7.3248-2.12115.38742.00092.4434-0.1427-0.0261-0.93630.17720.02580.42240.09790.07410.11690.1578-0.00010.01130.0621-0.00020.1025-6.06312.13228.658
30.62641.4536-0.795814.9817-7.0953.4297-0.07230.02710.0858-0.25170.15320.01720.076-0.1046-0.08090.17640.00070.03130.0781-0.00910.1015-7.18630.93520.725
43.7577-3.81583.133910.0458-4.37474.8446-0.0570.0053-0.1338-0.03150.15760.3392-0.16140.0293-0.10050.0983-0.0320.03020.0473-0.00660.0265-5.80522.23324.525
58.0194-3.794-2.98796.99252.179815.3296-0.0825-0.66550.02060.34180.1262-0.19650.05670.755-0.04360.0855-0.0133-0.0640.1391-0.01480.0618.54211.99330.295
63.8453-0.54772.0445.0646-9.655530.41340.16790.2824-0.1463-0.06070.2453-0.2828-0.2230.7113-0.41320.1606-0.0330.01520.1692-0.05430.20667.06117.316.138
70.86290.37280.56061.7461.02462.0783-0.0056-0.13840.11250.0494-0.025-0.0911-0.11270.03290.03050.1141-0.01060.01120.09290.00610.08050.33921.0917.992
87.8481-0.72866.0790.91470.14128.03530.12010.0375-0.182-0.0684-0.0867-0.12710.20630.0853-0.03350.1615-0.01160.02080.0490.01620.0742-3.90919.91421.478
910.2383-2.72330.79948.369-1.07135.3469-0.1287-0.1065-0.02170.1103-0.14540.29590.0367-0.31430.27410.07170.01020.05740.089-0.01690.0673-15.318.87715.614
104.92581.6616-13.75850.5786-5.533786.61410.439-1.09630.55310.1001-0.26030.1760.4906-3.4403-0.17880.2821-0.2040.03141.211-0.31650.62-21.4632.6429.619
1115.16821.50380.71016.0646-0.70045.31870.10210.4519-0.0133-0.5026-0.14480.48860.1829-0.31980.04270.1289-0.0107-0.03940.1341-0.01670.0591-14.2114.7832.602
128.26610.57841.34982.4364-0.75951.73470.04080.15960.1565-0.1882-0.1057-0.16650.0480.1060.06490.09380.01250.02210.07250.0170.03492.33310.4033.039
137.9564-2.2780.73193.019-0.29860.86220.07540.2635-0.0198-0.0049-0.06230.2058-0.0768-0.0202-0.01310.08940.00360.02420.0591-0.01370.0271-9.61610.71610.563
1413.83764.89853.41152.43091.17287.4561-0.40070.76620.3159-0.24050.2370.2953-0.6169-0.28770.16370.11710.0327-0.01770.11760.02110.0743-13.1914.5294.856
151.5871-0.80290.43882.0462-0.74082.0611-0.104-0.0620.04060.17140.0073-0.25050.04630.21090.09670.06420.026-0.01750.09550.00480.04596.343-0.0519.028
161.07310.2751-0.97271.3324-0.56131.9368-0.03070.0099-0.02570.0435-0.04920.0360.0108-0.00040.07990.09320.0050.0030.0438-0.0110.0381-4.016-3.46413.29
173.1969-1.4209-0.76935.1337-2.76789.9867-0.1509-0.1542-0.3097-0.078-0.1735-0.12850.72630.5680.32440.13170.05430.05030.03950.03790.1012.23-14.46416.332
180.96470.4818-0.37562.9798-0.57924.68550.01790.0432-0.0657-0.1258-0.07650.3130.1152-0.29140.05860.13820.00330.00830.0801-0.03270.0915-9.501-7.4024.55
192.3437-1.8771.19284.2039-1.4553.91190.05950.1814-0.0662-0.1092-0.1051-0.16960.04220.22770.04560.1095-0.00120.01560.0826-0.00570.02213.995-3.8562.336
2019.6837-1.10960.504624.20171.369124.48340.35171.3677-0.6296-0.9273-0.05291.11890.5082-0.5897-0.29870.24690.05-0.12790.1904-0.05510.0982-8.0581.244-6.688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A536 - 547
2X-RAY DIFFRACTION2A548 - 558
3X-RAY DIFFRACTION3A559 - 573
4X-RAY DIFFRACTION4A574 - 584
5X-RAY DIFFRACTION5A585 - 593
6X-RAY DIFFRACTION6A594 - 604
7X-RAY DIFFRACTION7A605 - 621
8X-RAY DIFFRACTION8A622 - 629
9X-RAY DIFFRACTION9A630 - 640
10X-RAY DIFFRACTION10A641 - 646
11X-RAY DIFFRACTION11A647 - 654
12X-RAY DIFFRACTION12A655 - 669
13X-RAY DIFFRACTION13A670 - 689
14X-RAY DIFFRACTION14A690 - 696
15X-RAY DIFFRACTION15A697 - 731
16X-RAY DIFFRACTION16A732 - 760
17X-RAY DIFFRACTION17A761 - 771
18X-RAY DIFFRACTION18A772 - 784
19X-RAY DIFFRACTION19A785 - 802
20X-RAY DIFFRACTION20A803 - 809

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