[English] 日本語
Yorodumi
- PDB-4fvp: Crystal structure of the Jak2 pseudokinase domain (apo form) -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more