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- PDB-7cml: The Crystal Structure of human JNK2 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 7cml
TitleThe Crystal Structure of human JNK2 from Biortus.
ComponentsMitogen-activated protein kinase 9
KeywordsTRANSFERASE / Protein kinase-like / transcription factor binding
Function / homology
Function and homology information


protein localization to tricellular tight junction / JUN kinase activity / inflammatory response to wounding / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / positive regulation of podosome assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / mitogen-activated protein kinase / JNK cascade ...protein localization to tricellular tight junction / JUN kinase activity / inflammatory response to wounding / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / positive regulation of podosome assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / mitogen-activated protein kinase / JNK cascade / cellular response to cadmium ion / protein serine/threonine/tyrosine kinase activity / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of protein ubiquitination / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / FCERI mediated MAPK activation / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / Signaling by ALK fusions and activated point mutants / regulation of circadian rhythm / cellular response to reactive oxygen species / cellular senescence / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Mitogen-activated protein kinase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWang, F. / Lin, D. / Cheng, W. / Miao, Q. / Huang, Y. / Shang, H.
CitationJournal: To Be Published
Title: The Crystal Structure of human JNK2 from Biortus.
Authors: Wang, F. / Lin, D. / Cheng, W. / Miao, Q. / Huang, Y. / Shang, H.
History
DepositionJul 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Structure summary / Category: citation / database_2 / struct
Item: _citation.title / _database_2.pdbx_DOI ..._citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 9
B: Mitogen-activated protein kinase 9


Theoretical massNumber of molelcules
Total (without water)87,8192
Polymers87,8192
Non-polymers00
Water3,009167
1
A: Mitogen-activated protein kinase 9


Theoretical massNumber of molelcules
Total (without water)43,9091
Polymers43,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase 9


Theoretical massNumber of molelcules
Total (without water)43,9091
Polymers43,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.004, 102.004, 70.088
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

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Components

#1: Protein Mitogen-activated protein kinase 9 / MAPK 9 / JNK-55 / Stress-activated protein kinase 1a / SAPK1a / Stress-activated protein kinase ...MAPK 9 / JNK-55 / Stress-activated protein kinase 1a / SAPK1a / Stress-activated protein kinase JNK2 / c-Jun N-terminal kinase 2


Mass: 43909.484 Da / Num. of mol.: 2 / Mutation: D3K, C6V, S8N, Q14E, K203A, E204A, K250A, K251A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK9, JNK2, PRKM9, SAPK1A / Production host: Escherichia coli (E. coli)
References: UniProt: P45984, mitogen-activated protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Na/K PO4, 20% PEG3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.15→19.616 Å / Num. obs: 39267 / % possible obs: 99.8 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 10.8
Reflection shellResolution: 2.15→2.22 Å / Rmerge(I) obs: 1.269 / Num. unique obs: 3435

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3npc

3npc


Resolution: 2.15→19.616 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.327 / WRfactor Rwork: 0.284 / SU B: 7.889 / SU ML: 0.196 / Average fsc free: 0.8972 / Average fsc work: 0.9186 / Cross valid method: FREE R-VALUE / ESU R: 0.381 / ESU R Free: 0.277
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3274 1929 4.913 %
Rwork0.2842 37335 -
all0.286 --
obs-39264 99.794 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.292 Å2
Baniso -1Baniso -2Baniso -3
1-0.703 Å2-0 Å2-0 Å2
2--0.703 Å2-0 Å2
3----1.406 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5406 0 0 167 5573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135560
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175250
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.647532
X-RAY DIFFRACTIONr_angle_other_deg1.1121.57612192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.27322.772285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.065151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1121530
X-RAY DIFFRACTIONr_chiral_restr0.0530.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021131
X-RAY DIFFRACTIONr_nbd_refined0.1890.21028
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.24810
X-RAY DIFFRACTIONr_nbtor_refined0.1550.22613
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2184
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.237
X-RAY DIFFRACTIONr_nbd_other0.1810.2150
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.212
X-RAY DIFFRACTIONr_mcbond_it1.7473.8092674
X-RAY DIFFRACTIONr_mcbond_other1.7463.8092673
X-RAY DIFFRACTIONr_mcangle_it2.9825.693327
X-RAY DIFFRACTIONr_mcangle_other2.9815.6913328
X-RAY DIFFRACTIONr_scbond_it1.6933.9852886
X-RAY DIFFRACTIONr_scbond_other1.6923.9842884
X-RAY DIFFRACTIONr_scangle_it2.9285.894201
X-RAY DIFFRACTIONr_scangle_other2.9275.894201
X-RAY DIFFRACTIONr_lrange_it5.02742.7836079
X-RAY DIFFRACTIONr_lrange_other5.02442.7816055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2060.4351420.4352761X-RAY DIFFRACTION99.9312
2.206-2.2660.4681410.4242665X-RAY DIFFRACTION99.9644
2.266-2.3320.4211490.42618X-RAY DIFFRACTION100
2.332-2.4040.461140.3792524X-RAY DIFFRACTION100
2.404-2.4830.4621400.3652478X-RAY DIFFRACTION100
2.483-2.570.4581300.3482335X-RAY DIFFRACTION99.9594
2.57-2.6670.381090.342286X-RAY DIFFRACTION100
2.667-2.7750.3311180.3242210X-RAY DIFFRACTION99.8713
2.775-2.8990.322890.3162144X-RAY DIFFRACTION100
2.899-3.040.3661010.2882042X-RAY DIFFRACTION100
3.04-3.2040.2611080.2611919X-RAY DIFFRACTION99.9014
3.204-3.3990.302950.2521828X-RAY DIFFRACTION100
3.399-3.6330.289850.2341720X-RAY DIFFRACTION100
3.633-3.9240.2481080.2271590X-RAY DIFFRACTION99.9411
3.924-4.2980.243700.2151465X-RAY DIFFRACTION99.9349
4.298-4.8040.202500.2021366X-RAY DIFFRACTION99.9294
4.804-5.5450.356700.2211182X-RAY DIFFRACTION100
5.545-6.7860.311420.2241017X-RAY DIFFRACTION99.9057
6.786-9.5760.256400.226797X-RAY DIFFRACTION99.7616
9.576-19.6160.291280.24388X-RAY DIFFRACTION86.3071

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