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- PDB-5awm: The Crystal Structure of JNK from Drosophila melanogaster Reveals... -

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Basic information

Entry
Database: PDB / ID: 5awm
TitleThe Crystal Structure of JNK from Drosophila melanogaster Reveals an Evolutionarily Conserved Topology with that of Mammalian JNK Proteins.
ComponentsStress-activated protein kinase JNK
KeywordsTRANSFERASE / c-Jun N-terminal kinase / MAP kinase / Drosophila JNK pathway
Function / homology
Function and homology information


collateral sprouting of injured axon / Formation of the cytosolic BSK 'scaffolding complex' / Formation of the nuclear AP-1 transcription factor 'scaffolding complex' / Transcriptional activtion by AP-1 transcription factor / Imd pathway / Activation of the AP-1 family of transcription factors / Interleukin-38 signaling / NRAGE signals death through JNK / chorion micropyle formation / embryonic anterior midgut (ectodermal) morphogenesis ...collateral sprouting of injured axon / Formation of the cytosolic BSK 'scaffolding complex' / Formation of the nuclear AP-1 transcription factor 'scaffolding complex' / Transcriptional activtion by AP-1 transcription factor / Imd pathway / Activation of the AP-1 family of transcription factors / Interleukin-38 signaling / NRAGE signals death through JNK / chorion micropyle formation / embryonic anterior midgut (ectodermal) morphogenesis / dorsal closure, spreading of leading edge cells / peptidoglycan recognition protein signaling pathway / imaginal disc fusion, thorax closure / imaginal disc-derived male genitalia morphogenesis / determination of digestive tract left/right asymmetry / FCERI mediated MAPK activation / Oxidative Stress Induced Senescence / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / melanization defense response / positive regulation of neuron remodeling / dorsal closure / mushroom body development / follicle cell of egg chamber development / JUN phosphorylation / dorsal appendage formation / positive regulation of border follicle cell migration / JUN kinase activity / engulfment of apoptotic cell / cellular response to arsenic-containing substance / axon extension / wound healing, spreading of epidermal cells / neuron development / long-term memory / MAP kinase activity / mitogen-activated protein kinase / vascular endothelial growth factor receptor signaling pathway / positive regulation of autophagy / JNK cascade / cellular response to cadmium ion / tumor necrosis factor-mediated signaling pathway / neuron projection morphogenesis / axon guidance / wound healing / cellular response to reactive oxygen species / cellular response to oxidative stress / antibacterial humoral response / response to heat / regulation of gene expression / response to oxidative stress / protein kinase activity / intracellular signal transduction / axon / protein serine/threonine kinase activity / dendrite / positive regulation of gene expression / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Stress-activated protein kinase JNK
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsBoonserm, P.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Mahidol University Thailand
CitationJournal: Bmc Struct.Biol. / Year: 2015
Title: The crystal structure of JNK from Drosophila melanogaster reveals an evolutionarily conserved topology with that of mammalian JNK proteins.
Authors: Chimnaronk, S. / Sitthiroongruang, J. / Srisucharitpanit, K. / Srisaisup, M. / Ketterman, A.J. / Boonserm, P.
History
DepositionJul 6, 2015Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 5, 2015ID: 4M3A
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stress-activated protein kinase JNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0644
Polymers45,5101
Non-polymers5553
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.486, 55.329, 126.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Stress-activated protein kinase JNK / dJNK / Protein basket


Mass: 45509.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: bsk, JNK, CG5680 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)pLysS
References: UniProt: P92208, mitogen-activated protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% (w/v) PEG 4000, 0.1 M Tris-HCl pH 8.5 and 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 28, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→28.28 Å / Num. obs: 51133 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.062 / Net I/av σ(I): 11.8 / Net I/σ(I): 0.118
Reflection shellResolution: 1.58→1.66 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1.8 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XS0

2xs0


Resolution: 1.79→28.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.468 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21956 3586 10.1 %RANDOM
Rwork0.17474 ---
obs0.17936 31789 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.457 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.79→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 33 143 2986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192904
X-RAY DIFFRACTIONr_bond_other_d0.0020.022741
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.9653938
X-RAY DIFFRACTIONr_angle_other_deg1.11536285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0865340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08723.836146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71915502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4221522
X-RAY DIFFRACTIONr_chiral_restr0.1280.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213242
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02691
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.712.3561375
X-RAY DIFFRACTIONr_mcbond_other2.7032.3531374
X-RAY DIFFRACTIONr_mcangle_it3.9013.5031710
X-RAY DIFFRACTIONr_mcangle_other3.8993.5051711
X-RAY DIFFRACTIONr_scbond_it3.7952.8361529
X-RAY DIFFRACTIONr_scbond_other3.7962.8371528
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7314.0812229
X-RAY DIFFRACTIONr_long_range_B_refined7.32219.3513260
X-RAY DIFFRACTIONr_long_range_B_other7.27419.2653209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 270 -
Rwork0.228 2318 -
obs--99.77 %

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