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- PDB-4ux9: Crystal structure of JNK1 bound to a MKK7 docking motif -

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Basic information

Entry
Database: PDB / ID: 4ux9
TitleCrystal structure of JNK1 bound to a MKK7 docking motif
Components
  • DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7
  • MITOGEN-ACTIVATED PROTEIN KINASE 8
KeywordsTRANSFERASE / JNK1 / INTRINSICALLY DISORDERED DOMAINS / MKK7
Function / homology
Function and homology information


positive regulation of cell killing / JUN phosphorylation / regulation of DNA replication origin binding / : / JUN kinase kinase activity / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / regulation of motor neuron apoptotic process / Activation of BIM and translocation to mitochondria ...positive regulation of cell killing / JUN phosphorylation / regulation of DNA replication origin binding / : / JUN kinase kinase activity / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / regulation of motor neuron apoptotic process / Activation of BIM and translocation to mitochondria / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / mitogen-activated protein kinase kinase / protein serine/threonine kinase binding / positive regulation of cyclase activity / histone deacetylase regulator activity / response to osmotic stress / positive regulation of NLRP3 inflammasome complex assembly / DSCAM interactions / NRAGE signals death through JNK / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / MAP kinase kinase activity / Uptake and function of anthrax toxins / MAP kinase activity / regulation of macroautophagy / mitogen-activated protein kinase / cellular response to interleukin-1 / response to tumor necrosis factor / stress-activated MAPK cascade / response to mechanical stimulus / response to UV / positive regulation of JUN kinase activity / JNK cascade / positive regulation of telomerase activity / cellular response to cadmium ion / positive regulation of telomere maintenance via telomerase / cellular response to amino acid starvation / positive regulation of protein metabolic process / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of protein binding / molecular function activator activity / FCERI mediated MAPK activation / positive regulation of JNK cascade / peptidyl-threonine phosphorylation / regulation of circadian rhythm / cellular response to reactive oxygen species / response to wounding / cellular response to mechanical stimulus / histone deacetylase binding / rhythmic process / regulation of protein localization / cellular senescence / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to oxidative stress / response to heat / protein phosphatase binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / response to oxidative stress / cellular response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / positive regulation of apoptotic process / axon / phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / synapse / apoptotic process / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / enzyme binding / signal transduction / mitochondrion / 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 / Dual specificity mitogen-activated protein kinase kinase 7 / Mitogen-activated protein kinase 8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsKragelj, J. / Palencia, A. / Nanao, M.H. / Maurin, D. / Bouvignies, G. / Blackledge, M. / Ringkjobing-Jensen, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure and Dynamics of the Mkk7-Jnk Signaling Complex.
Authors: Kragelj, J. / Palencia, A. / Nanao, M.H. / Maurin, D. / Bouvignies, G. / Blackledge, M. / Jensen, M.R.
History
DepositionAug 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Aug 19, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_site
Item: _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id ..._pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MITOGEN-ACTIVATED PROTEIN KINASE 8
B: MITOGEN-ACTIVATED PROTEIN KINASE 8
C: MITOGEN-ACTIVATED PROTEIN KINASE 8
D: MITOGEN-ACTIVATED PROTEIN KINASE 8
F: DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7
G: DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7
H: DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7
I: DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,51528
Polymers173,9548
Non-polymers3,56220
Water4,972276
1
A: MITOGEN-ACTIVATED PROTEIN KINASE 8
F: DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3797
Polymers43,4882
Non-polymers8905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MITOGEN-ACTIVATED PROTEIN KINASE 8
G: DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3797
Polymers43,4882
Non-polymers8905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MITOGEN-ACTIVATED PROTEIN KINASE 8
H: DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4758
Polymers43,4882
Non-polymers9876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MITOGEN-ACTIVATED PROTEIN KINASE 8
I: DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2836
Polymers43,4882
Non-polymers7944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.666, 180.159, 101.144
Angle α, β, γ (deg.)90.00, 110.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.7759, -0.1113, 0.6209), (0.1147, -0.9928, -0.03466), (0.6203, -0.04432, 0.7831)-53.07, 129, 175.5
2given(-0.7752, 0.0554, -0.6293), (0.07861, -0.98, -0.1831), (-0.6268, -0.1914, 0.7553)187.7, 133.4, 81.1
3given(-0.9999, -0.000405, -0.01685), (0.005495, 0.9529, 0.3032), (0.01593, 0.3033, -0.9528)130.8, -33.88, 216

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Components

#1: Protein
MITOGEN-ACTIVATED PROTEIN KINASE 8 / MAP KINASE 8 / MAPK 8 / JNK-46 / STRESS-ACTIVATED PROTEIN KINASE 1C / SAPK1C / STRESS-ACTIVATED ...MAP KINASE 8 / MAPK 8 / JNK-46 / STRESS-ACTIVATED PROTEIN KINASE 1C / SAPK1C / STRESS-ACTIVATED PROTEIN KINASE JNK1 / C-JUN N-TERMI NAL KINASE 1 / JNK1


Mass: 42096.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P45983, mitogen-activated protein kinase
#2: Protein/peptide
DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7 / MAP KINASE KINASE 7 / MAPKK 7 / JNK-ACTIVATING KINASE 2 / MAPK/ERK KINASE 7 / MEK 7 / STRESS- ...MAP KINASE KINASE 7 / MAPKK 7 / JNK-ACTIVATING KINASE 2 / MAPK/ERK KINASE 7 / MEK 7 / STRESS-ACTIVATED PROTEIN KINASE KINASE 4 / SAPK KINASE 4 / SAPKK-4 / SAPKK4 / C-JUN N-TERMINAL KINASE KINASE 2 / JNK KINASE 2 / JNKK 2 / MKK7


Mass: 1391.660 Da / Num. of mol.: 4 / Fragment: RESIDUES 37-48 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O14733
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.67 Å3/Da / Density % sol: 53.91 % / Description: NONE
Crystal growDetails: 50 MM HEPES 150 MM NACL 2 MM MGSO4 1 MM TCEP 2.6 M NH4SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2014 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 75436 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 66.09 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.66
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.66 / % possible all: 90.7

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XRW

2xrw


Resolution: 2.34→49.21 Å / Cor.coef. Fo:Fc: 0.9473 / Cor.coef. Fo:Fc free: 0.9308 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.285 / SU Rfree Blow DPI: 0.216 / SU Rfree Cruickshank DPI: 0.222
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 3985 5.28 %RANDOM
Rwork0.1999 ---
obs0.2021 75430 98.41 %-
Displacement parametersBiso mean: 66.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.0709 Å20 Å23.482 Å2
2--4.1542 Å20 Å2
3----2.0834 Å2
Refine analyzeLuzzati coordinate error obs: 0.329 Å
Refinement stepCycle: LAST / Resolution: 2.34→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11211 0 204 276 11691
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111660HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0915802HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5421SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes279HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1660HARMONIC5
X-RAY DIFFRACTIONt_it11660HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion3.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1490SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13046SEMIHARMONIC4
LS refinement shellResolution: 2.34→2.4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 0 %
Rwork0.2739 5036 -
all0.2739 5036 -
obs--98.41 %

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