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- PDB-2y8o: Crystal structure of human p38alpha complexed with a MAPK docking... -

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Basic information

Entry
Database: PDB / ID: 2y8o
TitleCrystal structure of human p38alpha complexed with a MAPK docking peptide
Components
  • DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 6
  • MITOGEN-ACTIVATED PROTEIN KINASE 14
KeywordsTRANSFERASE / SIGNALLING / MAP KINASE PATHWAY / PROTEIN-PROTEIN INTERACTION
Function / homology
Function and homology information


nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / mitogen-activated protein kinase kinase / stress-activated protein kinase signaling cascade / positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of synaptic membrane adhesion / negative regulation of cold-induced thermogenesis / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / CD163 mediating an anti-inflammatory response ...nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / mitogen-activated protein kinase kinase / stress-activated protein kinase signaling cascade / positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of synaptic membrane adhesion / negative regulation of cold-induced thermogenesis / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / CD163 mediating an anti-inflammatory response / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / positive regulation of myoblast fusion / cellular response to UV-B / cartilage condensation / mitogen-activated protein kinase p38 binding / positive regulation of muscle cell differentiation / Platelet sensitization by LDL / Myogenesis / positive regulation of myotube differentiation / NFAT protein binding / regulation of cytokine production involved in inflammatory response / Activation of the AP-1 family of transcription factors / D-glucose import / p38MAPK cascade / ERK/MAPK targets / PI5P Regulates TP53 Acetylation / response to dietary excess / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / Regulation of MITF-M-dependent genes involved in pigmentation / MAP kinase kinase activity / Uptake and function of anthrax toxins / signal transduction in response to DNA damage / regulation of ossification / MAP kinase activity / cellular response to vascular endothelial growth factor stimulus / RHO GTPases Activate NADPH Oxidases / mitogen-activated protein kinase / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / negative regulation of hippo signaling / positive regulation of myoblast differentiation / stress-activated MAPK cascade / skeletal muscle tissue development / positive regulation of cardiac muscle cell proliferation / cardiac muscle contraction / p38MAPK events / positive regulation of brown fat cell differentiation / striated muscle cell differentiation / response to muscle stretch / positive regulation of interleukin-12 production / osteoclast differentiation / positive regulation of erythrocyte differentiation / lipopolysaccharide-mediated signaling pathway / DNA damage checkpoint signaling / regulation of signal transduction by p53 class mediator / placenta development / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / positive regulation of D-glucose import / activated TAK1 mediates p38 MAPK activation / stem cell differentiation / negative regulation of inflammatory response to antigenic stimulus / negative regulation of canonical Wnt signaling pathway / NOD1/2 Signaling Pathway / response to insulin / bone development / PKR-mediated signaling / cellular response to virus / platelet activation / positive regulation of protein import into nucleus / VEGFA-VEGFR2 Pathway / Interleukin-1 signaling / glucose metabolic process / cell morphogenesis / positive regulation of reactive oxygen species metabolic process / chemotaxis / spindle pole / osteoblast differentiation / ADP signalling through P2Y purinoceptor 1 / cellular senescence / MAPK cascade / cellular response to lipopolysaccharide / protein tyrosine kinase activity / angiogenesis / secretory granule lumen / protein phosphatase binding / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / transcription by RNA polymerase II / cytoskeleton / cell surface receptor signaling pathway / regulation of cell cycle / positive regulation of MAPK cascade / intracellular signal transduction / nuclear speck / protein serine kinase activity
Similarity search - Function
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 / Serine/threonine-protein kinase, active site ...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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Dual specificity mitogen-activated protein kinase kinase 6 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBarkai, T. / Garai, A. / Toeroe, I. / Remenyi, A.
CitationJournal: Sci. Signal / Year: 2012
Title: Specificity of Linear Motifs that Bind to a Common Mitogen-Activated Protein Kinase Docking Groove.
Authors: Garai, A. / Zeke, A. / Gogl, G. / Toro, I. / Fordos, F. / Blankenburg, H. / Barkai, T. / Varga, J. / Alexa, A. / Emig, D. / Albrecht, M. / Remenyi, A.
History
DepositionFeb 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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: DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 6


Theoretical massNumber of molelcules
Total (without water)43,0282
Polymers43,0282
Non-polymers00
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-7.2 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.920, 81.920, 122.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2215-

HOH

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Components

#1: Protein MITOGEN-ACTIVATED PROTEIN KINASE 14 / CYTOKINE SUPPRESSIVE ANTI-INFLAMMATORY DRUG-BINDING PROTEIN / MAP KINASE MXI2 / MAX-INTERACTING ...CYTOKINE SUPPRESSIVE ANTI-INFLAMMATORY DRUG-BINDING PROTEIN / MAP KINASE MXI2 / MAX-INTERACTING PROTEIN 2 / MITOGEN-ACTIVATED PROTEIN KINASE P38 ALPHA


Mass: 41471.262 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET DERIVATIVE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS
References: UniProt: Q16539, mitogen-activated protein kinase
#2: Protein/peptide DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 6 / MAPK/ERK KINASE 6 / SAPKK3


Mass: 1556.937 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOCKING PEPTIDE OF MKK6, RESIDUES 4-17 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
References: UniProt: P52564, mitogen-activated protein kinase kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 85 TO SER

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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: 2.87 Å3/Da / Density % sol: 57 %
Description: FOUR WEDGES OF DATA WERE COLLECTED FROM A SINGLE CRYSTAL WITH MICRO-CRYSTAL DIFFRACTOMETER.
Crystal growpH: 7.5 / Details: 22% PEG3350 100MM HEPES 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 25, 2010 / Details: BENT MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→70.95 Å / Num. obs: 35294 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.86 % / Biso Wilson estimate: 27.36 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.18
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.04 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GC7

3gc7


Resolution: 1.95→46.38 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 20.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 1766 5 %
Rwork0.176 --
obs0.177 35282 99.9 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.93 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1-12.5244 Å20 Å20 Å2
2--12.5244 Å20 Å2
3---14.6599 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 0 293 3089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012885
X-RAY DIFFRACTIONf_angle_d1.1453921
X-RAY DIFFRACTIONf_dihedral_angle_d12.5851086
X-RAY DIFFRACTIONf_chiral_restr0.072441
X-RAY DIFFRACTIONf_plane_restr0.006503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00280.29091460.27012509X-RAY DIFFRACTION100
2.0028-2.06170.26621350.24152537X-RAY DIFFRACTION100
2.0617-2.12820.29361050.2152570X-RAY DIFFRACTION100
2.1282-2.20430.21261340.19292569X-RAY DIFFRACTION100
2.2043-2.29260.22511430.18122520X-RAY DIFFRACTION100
2.2926-2.39690.22581250.18112574X-RAY DIFFRACTION100
2.3969-2.52320.2331290.18582543X-RAY DIFFRACTION100
2.5232-2.68130.25181420.17532596X-RAY DIFFRACTION100
2.6813-2.88830.20181340.17472569X-RAY DIFFRACTION100
2.8883-3.17890.2231380.17732565X-RAY DIFFRACTION100
3.1789-3.63880.22671550.17042590X-RAY DIFFRACTION100
3.6388-4.58380.15511470.14092632X-RAY DIFFRACTION100
4.5838-46.39460.18481330.17092742X-RAY DIFFRACTION99
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)
1-0.0002-0.00070.00160.0015-0.00170.00050.0482-0.0080.00240.01750.0348-0.0330.0134-0.0155-00.0432-0.0174-0.0002-0.0349-0.10620.0107-17.270721.4763-8.6328
20.001-0.0004-0.0030.0003-0.00130.0050.0401-0.0082-0.0265-0.00860.03340.004-0.01280.002500.01850.00720.04450.044-0.00690.0349-37.096431.4511-2.1798
3-0.0046-0.00540.00210.00760.0034-00.0690.0349-0.1002-0.07250.10410.00940.0064-0.01540-0.07230.07340.0182-0.06560.1209-0.0493-45.626427.9024-4.8224
40.00010.0001-0.00010.00010.00010.0001-0.0006-0.0012-0.0001-0.0007-0.00050.0005-0.00090.0007-00.08430.00390.01050.077-0.00880.0761-27.396243.48056.7631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 6:104)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 105:203)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 204:355)
4X-RAY DIFFRACTION4CHAIN B

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