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- PDB-4fvq: Crystal structure of the Jak2 pseudokinase domain (Mg-ATP-bound form) -

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Basic information

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


interleukin-35-mediated signaling pathway / mineralocorticoid receptor signaling pathway / histone H3Y41 kinase activity / activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / symbiont-induced defense-related programmed cell death / mammary gland epithelium development / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / granulocyte macrophage colony-stimulating factor receptor complex ...interleukin-35-mediated signaling pathway / mineralocorticoid receptor signaling pathway / histone H3Y41 kinase activity / activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / symbiont-induced defense-related programmed cell death / mammary gland epithelium development / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / Signaling by Erythropoietin / interleukin-12 receptor binding / post-embryonic hemopoiesis / collagen-activated signaling pathway / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / interleukin-5-mediated signaling pathway / response to interleukin-12 / positive regulation of leukocyte proliferation / activation of Janus kinase activity / interleukin-12 receptor complex / interleukin-23 receptor complex / positive regulation of platelet aggregation / tyrosine phosphorylation of STAT protein / positive regulation of platelet activation / positive regulation of MHC class II biosynthetic process / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / type 1 angiotensin receptor binding / positive regulation of NK T cell proliferation / regulation of nitric oxide biosynthetic process / acetylcholine receptor binding / interleukin-12-mediated signaling pathway / interleukin-3-mediated signaling pathway / cellular response to interleukin-3 / Signaling by Leptin / positive regulation of signaling receptor activity / Interleukin-12 signaling / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / response to hydroperoxide / positive regulation of cell-substrate adhesion / negative regulation of cardiac muscle cell apoptotic process / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / positive regulation of epithelial cell apoptotic process / axon regeneration / peptide hormone receptor binding / growth hormone receptor signaling pathway / intrinsic apoptotic signaling pathway in response to oxidative stress / extrinsic component of plasma membrane / IFNG signaling activates MAPKs / Interleukin-20 family signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Interleukin-6 signaling / enzyme-linked receptor protein signaling pathway / interleukin-6-mediated signaling pathway / negative regulation of cell-cell adhesion / Prolactin receptor signaling / positive regulation of interleukin-17 production / negative regulation of DNA binding / MAPK3 (ERK1) activation / response to amine / positive regulation of nitric-oxide synthase biosynthetic process / MAPK1 (ERK2) activation / mesoderm development / positive regulation of natural killer cell proliferation / positive regulation of SMAD protein signal transduction / cell surface receptor signaling pathway via JAK-STAT / platelet-derived growth factor receptor signaling pathway / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / growth hormone receptor signaling pathway via JAK-STAT / response to tumor necrosis factor / Interleukin receptor SHC signaling / phosphatidylinositol 3-kinase binding / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / Erythropoietin activates RAS / Growth hormone receptor signaling / extrinsic apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / Signaling by CSF3 (G-CSF) / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of T cell proliferation / tumor necrosis factor-mediated signaling pathway / actin filament polymerization / extrinsic component of cytoplasmic side of plasma membrane / SH2 domain binding / cellular response to dexamethasone stimulus / post-translational protein modification / erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of interleukin-1 beta production / caveola / endosome lumen / positive regulation of cell differentiation
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 / Jak1 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 / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / SH2 domain / 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 / 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
ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / Tyrosine-protein kinase JAK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7715
Polymers33,1211
Non-polymers6504
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.632, 57.548, 60.967
Angle α, β, γ (deg.)90.000, 110.850, 90.000
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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris/HCl, PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 29027 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.066 / Χ2: 0.77 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.785.30.43113760.548193.6
1.78-1.815.60.41613740.534196
1.81-1.855.60.36814030.529197.4
1.85-1.896.20.33914350.501199.3
1.89-1.936.30.27114680.537199.9
1.93-1.976.40.23814730.5771100
1.97-2.026.20.21714310.595199.8
2.02-2.076.70.17714490.613199.9
2.07-2.146.70.15614740.6311100
2.14-2.26.40.12814590.6851100
2.2-2.286.60.11214430.677199.9
2.28-2.386.80.09714540.6941100
2.38-2.486.60.08714600.7111100
2.48-2.616.70.07914710.761100
2.61-2.786.80.06914660.8031100
2.78-2.996.60.06514470.9771100
2.99-3.296.90.05614611.0621100
3.29-3.776.70.04614761.199199.9
3.77-4.756.70.04114821.2951100
4.75-506.60.03615251.1981100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M14

1m14


Resolution: 1.75→41.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1942 / WRfactor Rwork: 0.1706 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8581 / SU B: 4.592 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1113 / SU Rfree: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1987 1471 5.1 %RANDOM
Rwork0.1748 ---
obs0.176 29014 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 84.44 Å2 / Biso mean: 31.2572 Å2 / Biso min: 14.98 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å20 Å20.33 Å2
2---1.84 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.75→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 40 147 2322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022222
X-RAY DIFFRACTIONr_bond_other_d0.0060.021454
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9783026
X-RAY DIFFRACTIONr_angle_other_deg0.86233561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0885273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6524.902102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01115359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0141510
X-RAY DIFFRACTIONr_chiral_restr0.080.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02437
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 105 -
Rwork0.241 1847 -
all-1952 -
obs--92.64 %
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)
15.29221.544-2.36347.5479-1.08882.9559-0.0361-0.01640.17120.01780.0184-0.197-0.1250.2360.01770.079-0.0177-0.02620.0991-0.01220.0285-2.87524.15427.04
20.2379-0.0002-0.33887.0659-1.2580.93080.0686-0.00620.1256-0.04590.0248-0.0105-0.070.0547-0.09350.07590.00010.00750.0798-0.00120.1238-5.79226.43822.228
32.5432-1.2626-0.18882.98550.54191.63860.0386-0.22080.09620.26170.1182-0.15560.05470.2265-0.15690.0833-0.0244-0.03990.0971-0.02820.04120.79216.82427.815
43.8802-0.62455.55035.4836-12.745334.13080.62420.5239-0.08830.09880.12270.30870.3130.4819-0.74680.2703-0.05030.00490.2699-0.02130.26337.23216.93416.576
51.58370.35131.41322.11831.10443.17310.0849-0.1230.08540.07670.0429-0.2392-0.1623-0.0181-0.12780.0682-0.02810.01230.10.00620.10680.33921.0917.992
610.1101-0.26497.48073.49661.22886.69390.2151-0.1548-0.1182-0.32890.0086-0.29970.0250.0025-0.22380.0505-0.01860.02220.0693-0.00350.0526-3.90919.91421.478
74.9562-0.9883-0.257212.9759-0.75135.5427-0.1015-0.075-0.14410.18240.13810.25860.0824-0.3723-0.03660.02480.00030.03730.1166-0.00340.0935-15.318.87715.614
81.632-0.7999-9.79560.39784.819358.8525-0.05910.1550.00010.0092-0.11170.06010.2242-0.99060.17080.2117-0.2054-0.17640.5745-0.00430.6976-21.4632.6429.619
99.75692.337-0.19593.1722-0.30021.25060.0130.1921-0.0184-0.3569-0.07480.00210.0186-0.08970.06180.06430.0294-0.00710.08770.01440.0259-4.248.2042.626
103.3964-0.9424-0.47662.4272-0.10391.42360.05540.2290.1003-0.0514-0.01820.1905-0.0814-0.1686-0.03720.0220.0029-0.01480.08350.00130.0686-9.95411.2719.231
111.5584-1.15720.18622.2838-0.73041.3494-0.1345-0.130.04870.22660.0519-0.2609-0.02360.17090.08260.02670.0136-0.0330.130.00530.07134.8871.35117.955
121.4165-0.1248-0.88881.983-0.0510.8383-0.0457-0.0003-0.06670.04650.00170.05440.01670.02830.04390.03530.0076-0.00980.0747-0.00330.0597-4.016-3.46413.29
133.045-0.216-1.46977.8628-2.39219.5565-0.1681-0.2412-0.4261-0.0206-0.1331-0.19540.59850.48220.30120.07090.06370.04520.06440.05750.12312.558-14.6317.029
141.4714-0.4267-0.15381.64330.38721.86090.03380.154-0.0952-0.147-0.10030.02870.09760.01740.06650.06720.01660.0060.074-0.00580.051-1.09-5.4663.375
1522.5323-3.1612-2.400219.96272.723820.33270.56151.1666-0.7431-1.0915-0.61140.98320.4133-0.59020.04990.26910.1008-0.13180.1946-0.07660.0869-8.0581.244-6.688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A536 - 553
2X-RAY DIFFRACTION2A554 - 574
3X-RAY DIFFRACTION3A575 - 592
4X-RAY DIFFRACTION4A593 - 604
5X-RAY DIFFRACTION5A605 - 621
6X-RAY DIFFRACTION6A622 - 629
7X-RAY DIFFRACTION7A630 - 640
8X-RAY DIFFRACTION8A641 - 646
9X-RAY DIFFRACTION9A647 - 668
10X-RAY DIFFRACTION10A669 - 693
11X-RAY DIFFRACTION11A694 - 731
12X-RAY DIFFRACTION12A732 - 760
13X-RAY DIFFRACTION13A761 - 770
14X-RAY DIFFRACTION14A771 - 802
15X-RAY DIFFRACTION15A803 - 809

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