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- PDB-4fvr: Crystal structure of the Jak2 pseudokinase domain mutant V617F (M... -

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Basic information

Entry
Database: PDB / ID: 4fvr
TitleCrystal structure of the Jak2 pseudokinase domain mutant V617F (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 / intracellular 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 / intracellular 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 / acetylcholine receptor binding / interleukin-12-mediated signaling pathway / interleukin-3-mediated signaling pathway / regulation of nitric oxide biosynthetic process / 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 / positive regulation of cell-substrate adhesion / response to hydroperoxide / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / negative regulation of cardiac muscle cell apoptotic process / 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 / positive regulation of apoptotic signaling pathway / extrinsic 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
ADENOSINE-5'-TRIPHOSPHATE / Tyrosine-protein kinase JAK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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_seq_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

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Assembly

Deposited unit
A: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8163
Polymers33,2841
Non-polymers5312
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.900, 57.326, 60.555
Angle α, β, γ (deg.)90.00, 111.86, 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: 33284.133 Da / Num. of mol.: 1 / Fragment: Jak2 pseudokinase domain, UNP residues 536-812 / Mutation: V617F, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: Feb 12, 2012
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 4FVP

4fvp


Resolution: 2→43.5 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.1783 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8386 / SU B: 8.55 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1842 / SU Rfree: 0.1661 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1006 5.2 %RANDOM
Rwork0.1806 18524 --
obs0.1831 19530 95.5 %-
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: 130.49 Å2 / Biso mean: 36.77 Å2 / Biso min: 19.04 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å2-3.53 Å2
2---2.51 Å20 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 2→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 0 32 111 2290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022231
X-RAY DIFFRACTIONr_bond_other_d0.0060.021466
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9733040
X-RAY DIFFRACTIONr_angle_other_deg0.83733590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7185273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08224.902102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68915363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.649159
X-RAY DIFFRACTIONr_chiral_restr0.0720.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02444
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 40 -
Rwork0.252 921 -
all-961 -
obs--64.2 %
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)
14.23541.39661.58284.4425-0.68081.7610.1548-0.1409-0.22590.19960.0422-0.00560.0574-0.168-0.1970.1347-0.01330.01410.07540.03790.08524.296-24.27726.686
20.6748-0.10830.39823.8161-0.31250.68230.0633-0.1124-0.19690.02380.01760.07390.0446-0.1572-0.08090.139-0.0054-0.00350.08740.03530.15376.413-24.4422.696
34.41075.71724.773430.8727.24955.2190.19170.6579-0.5464-0.2710.4445-1.21670.15510.7028-0.63620.23270.05070.04230.2742-0.06680.358911.109-33.0919.642
48.82190.0411-2.87714.47271.38887.3397-0.0613-0.3840.12570.49420.05880.0128-0.1656-0.31760.00240.20680.00850.04190.22770.01720.10691.714-17.10127.785
54.3953-5.4492-1.554522.6634-5.984.481-0.19950.1347-0.20481.77290.06090.1194-0.6899-0.18120.13860.26270.01690.13930.4884-0.03080.2038-8.289-12.16431.094
60.9707-0.13630.10921.065-0.28752.85280.0164-0.1396-0.1540.09370.06780.11870.1611-0.1719-0.08420.0479-0.01680.05020.13920.0130.1286-2.64-19.44417.16
73.19031.8442-0.7332.8801-1.34542.4797-0.0349-0.08760.05150.08520.0165-0.12120.00890.06880.01840.04880.03220.02410.1255-0.01750.129310.381-14.71718.401
81.12522.98064.12978.055311.388916.4315-0.19150.0763-0.2148-0.15060.4008-0.3338-0.10621.1487-0.20930.130.08320.11170.72970.36320.552221.446-2.7517.477
910.5551.3972-0.61792.7581-0.46740.7651-0.06250.2080.0406-0.27310.0477-0.17250.04590.11980.01470.06750.02930.06540.15020.00380.07978.193-7.3841.656
102.7739-1.05151.19372.75470.43681.9906-0.0285-0.04620.04040.07350.0133-0.01650.0012-0.03890.01510.0609-0.00420.05860.11770.02010.06552.073-10.4119.585
1138.8202-12.444615.578424.53934.853138.56810.90512.9552-0.1358-1.6131-0.2507-2.03520.44152.9882-0.65440.35750.1390.2240.7592-0.06290.496121.71-14.2920.284
125.5403-1.503-2.85081.69920.80855.0224-0.08810.04930.20540.18570.2283-0.05380.1820.0464-0.14020.0529-0.00170.04370.1437-0.01260.13684.619-12.68312.184
132.96540.2438-1.43153.9376-3.03172.8617-0.2262-0.2669-0.0740.42290.23720.0661-0.2304-0.0807-0.0110.16310.10670.06970.2424-0.0320.1282-4.151.60420.783
146.0974-2.2811-4.91765.75416.275310.8641-0.3446-0.0395-0.2318-0.1411-0.27940.42310.1303-0.92390.6240.14560.11250.08680.33430.00350.2074-11.6741.66114.969
153.2067-0.96641.51441.857-0.76211.6663-0.0876-0.00410.14750.22090.0344-0.1057-0.10470.01160.05320.07090.02060.05110.1312-0.00810.10544.1731.1429.195
162.30590.18740.65955.22030.14434.2695-0.4008-0.12070.06470.1340.131-0.0292-0.3270.18570.26980.13350.0288-0.03370.0897-0.01410.15657.9897.77920.276
174.49392.23533.60675.89943.89814.4286-0.2957-0.48080.63260.0791-0.010.0545-0.6598-0.6980.30570.1720.1224-0.07780.1102-0.08260.1703-1.72714.29317.845
187.09862.2799-0.93322.09430.40916.0453-0.24670.1750.3567-0.0142-0.0019-0.3393-0.24780.47130.24860.145-0.0199-0.0440.08680.07580.224810.3968.5885.778
192.0295-0.07010.66070.38520.14051.55050.00730.05770.07010.06110.06440.00710.0526-0.1195-0.07170.09650.00850.03590.13480.01110.1127-2.5395.0772.886
2012.2201-2.7359-2.09053.96952.116312.31210.580.72950.713-0.6521-0.15370.0157-0.47620.3617-0.42630.22050.00940.05380.19390.03920.12195.706-1.927-5.653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A536 - 554
2X-RAY DIFFRACTION2A555 - 570
3X-RAY DIFFRACTION3A571 - 578
4X-RAY DIFFRACTION4A579 - 585
5X-RAY DIFFRACTION5A586 - 591
6X-RAY DIFFRACTION6A592 - 620
7X-RAY DIFFRACTION7A621 - 639
8X-RAY DIFFRACTION8A640 - 647
9X-RAY DIFFRACTION9A648 - 662
10X-RAY DIFFRACTION10A663 - 684
11X-RAY DIFFRACTION11A685 - 692
12X-RAY DIFFRACTION12A693 - 702
13X-RAY DIFFRACTION13A703 - 723
14X-RAY DIFFRACTION14A724 - 732
15X-RAY DIFFRACTION15A733 - 749
16X-RAY DIFFRACTION16A750 - 759
17X-RAY DIFFRACTION17A760 - 770
18X-RAY DIFFRACTION18A771 - 780
19X-RAY DIFFRACTION19A781 - 800
20X-RAY DIFFRACTION20A801 - 809

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