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- PDB-8yp4: Structure of MAP2K1 complexed with 5Z7-oxozeaenol -

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Basic information

Entry
Database: PDB / ID: 8yp4
TitleStructure of MAP2K1 complexed with 5Z7-oxozeaenol
ComponentsDual specificity mitogen-activated protein kinase kinase 1
KeywordsTRANSFERASE / Mitogen-activated protein kinase kinase 1
Function / homology
Function and homology information


negative regulation of homotypic cell-cell adhesion / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / regulation of vascular associated smooth muscle contraction / mitogen-activated protein kinase kinase / positive regulation of muscle contraction / Golgi inheritance / placenta blood vessel development / MAP kinase scaffold activity ...negative regulation of homotypic cell-cell adhesion / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / regulation of vascular associated smooth muscle contraction / mitogen-activated protein kinase kinase / positive regulation of muscle contraction / Golgi inheritance / placenta blood vessel development / MAP kinase scaffold activity / regulation of axon regeneration / cerebellar cortex formation / labyrinthine layer development / melanosome transport / Signaling by MAP2K mutants / type B pancreatic cell proliferation / central nervous system neuron differentiation / vesicle transport along microtubule / positive regulation of Ras protein signal transduction / regulation of Golgi inheritance / mitogen-activated protein kinase kinase kinase binding / positive regulation of axonogenesis / trachea formation / triglyceride homeostasis / regulation of early endosome to late endosome transport / Negative feedback regulation of MAPK pathway / regulation of stress-activated MAPK cascade / Frs2-mediated activation / MAPK3 (ERK1) activation / ERBB2-ERBB3 signaling pathway / face development / MAP kinase kinase activity / endodermal cell differentiation / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Bergmann glial cell differentiation / positive regulation of protein serine/threonine kinase activity / thyroid gland development / positive regulation of ATP biosynthetic process / Uptake and function of anthrax toxins / protein kinase activator activity / response to axon injury / Schwann cell development / keratinocyte differentiation / neuron projection morphogenesis / ERK1 and ERK2 cascade / myelination / protein serine/threonine/tyrosine kinase activity / insulin-like growth factor receptor signaling pathway / positive regulation of autophagy / response to glucocorticoid / dendrite cytoplasm / thymus development / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Signal transduction by L1 / protein serine/threonine kinase activator activity / cell motility / positive regulation of transcription elongation by RNA polymerase II / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / small GTPase binding / chemotaxis / neuron differentiation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cellular senescence / Signaling by BRAF and RAF1 fusions / late endosome / MAPK cascade / heart development / protein tyrosine kinase activity / response to oxidative stress / scaffold protein binding / cell cortex / microtubule / perikaryon / early endosome / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / postsynaptic density / positive regulation of cell migration / ciliary basal body / negative regulation of cell population proliferation / negative regulation of gene expression / axon / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / positive regulation of gene expression / centrosome / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / Golgi apparatus / signal transduction / mitochondrion
Similarity search - Function
: / 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
Similarity search - Domain/homology
: / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsYumura, S. / Kinoshita, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2024
Title: Conserved gatekeeper methionine regulates the binding and access of kinase inhibitors to ATP sites of MAP2K1, 4, and 7: Clues for developing selective inhibitors.
Authors: Yumura, S. / Kitagawa, D. / Moritsugu, K. / Nakayama, A. / Shinada, T. / Sawa, M. / Kinoshita, T.
History
DepositionMar 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity mitogen-activated protein kinase kinase 1
B: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4935
Polymers81,6722
Non-polymers8213
Water2,468137
1
A: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2002
Polymers40,8361
Non-polymers3641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2923
Polymers40,8361
Non-polymers4562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.364, 128.947, 65.689
Angle α, β, γ (deg.)90.00, 94.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dual specificity mitogen-activated protein kinase kinase 1 / MAP kinase kinase 1 / MAPKK 1 / MKK1 / ERK activator kinase 1 / MAPK/ERK kinase 1 / MEK 1


Mass: 40835.996 Da / Num. of mol.: 2 / Mutation: T286A, T292A, S298A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q02750, mitogen-activated protein kinase kinase
#2: Chemical ChemComp-WNT / (4~{S},9~{S},10~{S},12~{E})-16-methoxy-4-methyl-9,10,18-tris(oxidanyl)-3-oxabicyclo[12.4.0]octadeca-1(18),12,14,16-tetraene-2,8-dione


Mass: 364.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 8% Tacsimete pH 5.0, 19.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.35→47.194 Å / Num. obs: 32615 / % possible obs: 99.6 % / Redundancy: 4 % / CC1/2: 0.997 / Net I/σ(I): 10.15
Reflection shellResolution: 2.35→2.49 Å / Num. unique obs: 17348 / CC1/2: 0.573

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→45.93 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.533 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28403 1629 5 %RANDOM
Rwork0.20631 ---
obs0.21023 30955 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.273 Å2
Baniso -1Baniso -2Baniso -3
1--3.47 Å20 Å21.77 Å2
2---3.69 Å2-0 Å2
3---6.76 Å2
Refinement stepCycle: 1 / Resolution: 2.35→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4832 0 0 137 4969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124932
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164834
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.8526627
X-RAY DIFFRACTIONr_angle_other_deg0.5481.7811183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.871528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88410921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.210.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021054
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_it6.9039.4042412
X-RAY DIFFRACTIONr_mcbond_other6.9029.4042412
X-RAY DIFFRACTIONr_mcangle_it10.65216.8673001
X-RAY DIFFRACTIONr_mcangle_other10.6516.873002
X-RAY DIFFRACTIONr_scbond_it6.33910.0482520
X-RAY DIFFRACTIONr_scbond_other6.33810.0482520
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.19218.2623627
X-RAY DIFFRACTIONr_long_range_B_refined15.46790.045575
X-RAY DIFFRACTIONr_long_range_B_other15.47890.095564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.409 Å
RfactorNum. reflection% reflection
Rfree0.434 116 -
Rwork0.433 2211 -
obs--98.48 %

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