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- PDB-4ka3: Structure of MAP kinase in complex with a docking peptide -

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Basic information

Entry
Database: PDB / ID: 4ka3
TitleStructure of MAP kinase in complex with a docking peptide
Components
  • Mitogen-activated protein kinase 14
  • TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
KeywordsTRANSFERASE/PROTEIN BINDING / kinase domain / phosphorylation / KIM / TRANSFERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / myoblast differentiation involved in skeletal muscle regeneration / Regulation of MITF-M-dependent genes involved in pigmentation / NLRP1 inflammasome complex assembly / cell surface receptor protein serine/threonine kinase signaling pathway / ADP signalling through P2Y purinoceptor 1 ...p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / myoblast differentiation involved in skeletal muscle regeneration / Regulation of MITF-M-dependent genes involved in pigmentation / NLRP1 inflammasome complex assembly / cell surface receptor protein serine/threonine kinase signaling pathway / ADP signalling through P2Y purinoceptor 1 / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence / Myogenesis / Regulation of TP53 Activity through Phosphorylation / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / response to muramyl dipeptide / VEGFA-VEGFR2 Pathway / regulation of ossification / chondrocyte differentiation / fatty acid oxidation / striated muscle cell differentiation / positive regulation of cGAS/STING signaling pathway / regulation of synaptic membrane adhesion / stress-induced premature senescence / positive regulation of myoblast fusion / cartilage condensation / stress-activated protein kinase signaling cascade / skeletal muscle tissue development / positive regulation of cyclase activity / positive regulation of myotube differentiation / response to dietary excess / serine/threonine protein kinase complex / cellular response to UV-B / mitogen-activated protein kinase p38 binding / non-canonical NF-kappaB signal transduction / NFAT protein binding / regulation of cytokine production involved in inflammatory response / cellular response to lipoteichoic acid / p38MAPK cascade / positive regulation of cardiac muscle cell proliferation / response to muscle stretch / protein serine/threonine phosphatase activity / MAP kinase activity / cellular response to vascular endothelial growth factor stimulus / regulation of MAPK cascade / mitogen-activated protein kinase / lipopolysaccharide-mediated signaling pathway / positive regulation of brown fat cell differentiation / vascular endothelial growth factor receptor signaling pathway / pyroptotic inflammatory response / stress-activated MAPK cascade / positive regulation of myoblast differentiation / negative regulation of hippo signaling / placenta development / osteoclast differentiation / positive regulation of interleukin-12 production / cell morphogenesis / DNA damage checkpoint signaling / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / Neutrophil degranulation / positive regulation of D-glucose import across plasma membrane / positive regulation of erythrocyte differentiation / IRAK2 mediated activation of TAK1 complex / protein serine/threonine kinase activator activity / Alpha-protein kinase 1 signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / tumor necrosis factor-mediated signaling pathway / glucose metabolic process / TRAF6-mediated induction of TAK1 complex within TLR4 complex / response to insulin / cellular response to ionizing radiation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / cellular response to tumor necrosis factor / TNFR1-induced NF-kappa-B signaling pathway / cellular response to virus / activated TAK1 mediates p38 MAPK activation / positive regulation of protein import into nucleus / negative regulation of canonical Wnt signaling pathway / protein maturation / bone development / peptidyl-serine phosphorylation / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / kinase activity / positive regulation of reactive oxygen species metabolic process / CLEC7A (Dectin-1) signaling / osteoblast differentiation / FCERI mediated NF-kB activation / Interleukin-1 signaling / angiogenesis / MAPK cascade / protein autophosphorylation / cellular response to lipopolysaccharide / response to lipopolysaccharide / spindle pole / protein phosphatase binding / molecular adaptor activity
Similarity search - Function
Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. ...Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / 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
Mitogen-activated protein kinase 14 / TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.707 Å
AuthorsXin, F.J. / Wu, J.W.
CitationJournal: Sci China Life Sci / Year: 2013
Title: Crystal structure of the p38 alpha MAP kinase in complex with a docking peptide from TAB1
Authors: Xin, F.J. / Wu, J.W.
History
DepositionApr 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 14
B: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1


Theoretical massNumber of molelcules
Total (without water)44,5072
Polymers44,5072
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-9 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.148, 82.148, 122.556
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Mitogen-activated protein kinase 14 / MAP kinase 14 / MAPK 14 / CRK1 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha


Mass: 41338.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P47811, mitogen-activated protein kinase
#2: Protein/peptide TGF-beta-activated kinase 1 and MAP3K7-binding protein 1


Mass: 3168.479 Da / Num. of mol.: 1 / Fragment: UNP residues 395-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAB1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15750
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.86
Details: 100mM Hepes, 22% polyacrylic acid 5100, pH 7.86, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979413 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979413 Å / Relative weight: 1
ReflectionResolution: 2.707→50 Å / Num. all: 13030 / Num. obs: 13001 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 61.93 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.1
Reflection shellResolution: 2.71→2.76 Å / Redundancy: 6 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.9 / Num. unique all: 662 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LEZ

1lez


Resolution: 2.707→26.827 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.79 / SU ML: 0.44 / σ(F): 1.34 / Phase error: 26.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 648 4.98 %RANDOM
Rwork0.225 ---
all0.225 13030 --
obs0.227 13001 96.13 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.625 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 121.07 Å2 / Biso mean: 70.358 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-1.7664 Å20 Å2-0 Å2
2--1.7664 Å20 Å2
3----2.0909 Å2
Refinement stepCycle: LAST / Resolution: 2.707→26.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 0 8 2807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012863
X-RAY DIFFRACTIONf_angle_d1.2413886
X-RAY DIFFRACTIONf_chiral_restr0.074439
X-RAY DIFFRACTIONf_plane_restr0.005496
X-RAY DIFFRACTIONf_dihedral_angle_d17.5631063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.707-2.91570.38251360.333325072643100
2.9157-3.20870.35751450.303125212666100
3.2087-3.6720.30781310.26422245237689
3.672-4.62250.21471130.19832455256895
4.6225-26.8280.23061230.18712625274897
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)
14.46040.9574-0.97393.676-0.82562.09550.1936-0.33780.20490.55740.09230.6759-0.3682-0.0331-0.29010.5417-0.0534-0.00560.35640.0260.387317.5047-21.8959-9.2469
23.8035-4.4423.24547.6343-6.37075.4798-0.1767-0.50950.3414-0.04330.32270.0918-0.0313-0.6596-0.33320.507-0.05720.03650.60790.00930.451727.7439-34.5973.5633
34.49931.31721.70383.05370.90762.7276-0.1199-0.20010.5209-0.13030.0439-0.2023-0.06750.16450.0320.41610.07390.03530.4409-0.05580.467846.6383-27.96050.1397
43.497-2.70021.65973.7224-1.61423.42220.14630.1153-0.1263-0.39730.0724-0.06570.30920.3453-0.17710.4348-0.03050.03840.4042-0.05290.332637.7626-30.3533-13.2165
56.95873.14711.24323.8373-3.01715.5694-0.06050.0821-1.6961-0.1777-0.72960.91410.5324-0.84930.45570.5446-0.08990.07450.6198-0.01010.574727.0308-43.99386.6921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 4:102)A4 - 102
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 103:123)A103 - 123
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 124:278)A124 - 278
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 279:354)A279 - 354
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 406:413)B406 - 413

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