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- PDB-5hze: Mek1 adopts DFG-out conformation when bound to an analog of E6201. -

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Basic information

Entry
Database: PDB / ID: 5hze
TitleMek1 adopts DFG-out conformation when bound to an analog of E6201.
ComponentsDual specificity mitogen-activated protein kinase kinase 1
KeywordsTransferase/Transferase Inhibitor / Mek1 / E6201 / Covalent inhibitor / kinase / Mek-1 / MAP2K1 / DFG-out / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


negative regulation of homotypic cell-cell adhesion / regulation of vascular associated smooth muscle contraction / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / mitogen-activated protein kinase kinase / melanosome transport / Golgi inheritance / MAP kinase scaffold activity / positive regulation of muscle contraction / Signaling by MAP2K mutants / vesicle transport along microtubule ...negative regulation of homotypic cell-cell adhesion / regulation of vascular associated smooth muscle contraction / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / mitogen-activated protein kinase kinase / melanosome transport / Golgi inheritance / MAP kinase scaffold activity / positive regulation of muscle contraction / Signaling by MAP2K mutants / vesicle transport along microtubule / regulation of Golgi inheritance / mitogen-activated protein kinase kinase kinase binding / 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 / positive regulation of protein serine/threonine kinase activity / MAP kinase kinase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular junction development / positive regulation of ATP biosynthetic process / response to axon injury / Uptake and function of anthrax toxins / ERK1 and ERK2 cascade / protein kinase activator activity / Schwann cell development / myelination / neuron projection morphogenesis / insulin-like growth factor receptor signaling pathway / protein serine/threonine/tyrosine kinase activity / positive regulation of autophagy / response to glucocorticoid / dendrite cytoplasm / Signal transduction by L1 / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / positive regulation of transcription elongation by RNA polymerase II / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cellular senescence / 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 / MAPK cascade / Signaling by BRAF and RAF1 fusions / late endosome / protein tyrosine kinase activity / response to oxidative stress / scaffold protein binding / cell cortex / ciliary basal body / microtubule / early endosome / perikaryon / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / postsynaptic density / positive regulation of cell migration / negative regulation of cell population proliferation / negative regulation of gene expression / protein serine kinase activity / axon / focal adhesion / protein serine/threonine kinase activity / centrosome / positive regulation of gene expression / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / glutamatergic synapse / signal transduction / endoplasmic reticulum / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / 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. ...: / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-E62 / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLarsen, N.A. / Bloudoff, K.
CitationJournal: To Be Published
Title: Mek1 adopts DFG-out conformation when bound to an analog of E6201.
Authors: Larsen, N.A. / Bloudoff, K. / Subramanian, V. / Nomoto, K. / Wang, J.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3614
Polymers38,9351
Non-polymers4263
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.118, 77.118, 222.064
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-403-

MG

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Components

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


Mass: 38934.871 Da / Num. of mol.: 1 / Mutation: S298N, S299K, Y300F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q02750, mitogen-activated protein kinase kinase
#2: Chemical ChemComp-E62 / (3S,4R,8S,9S,11E)-8,9,16-trihydroxy-3,4-dimethyl-14-(methylamino)-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione


Mass: 377.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27NO6
#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


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris pH 8.0, 180 mM CaCl2, 14-18% PEG 4000. Co-crystallized with 1mM ATPgammaS (30 mM stock formulated in H2O). Crystals backsoaked for 2 weeks in 1 mM compound 3.3% DMSO final.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16108 / % possible obs: 100 % / Redundancy: 17.1 % / Net I/σ(I): 26.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→42.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.908 / SU B: 9.117 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.282 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28714 822 5.2 %RANDOM
Rwork0.20053 ---
obs0.20498 15135 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.241 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å21.01 Å20 Å2
2--2.02 Å20 Å2
3----6.55 Å2
Refinement stepCycle: 1 / Resolution: 2.4→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 29 34 2422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192439
X-RAY DIFFRACTIONr_bond_other_d0.0030.022363
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.9873290
X-RAY DIFFRACTIONr_angle_other_deg1.4263.0045450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54124.762105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30815432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6951513
X-RAY DIFFRACTIONr_chiral_restr0.0950.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212732
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02527
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_it5.5036.8151219
X-RAY DIFFRACTIONr_mcbond_other5.4886.8111218
X-RAY DIFFRACTIONr_mcangle_it8.15910.1961519
X-RAY DIFFRACTIONr_mcangle_other8.15710.2011520
X-RAY DIFFRACTIONr_scbond_it6.0767.2191220
X-RAY DIFFRACTIONr_scbond_other6.0747.2171221
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.11910.6081771
X-RAY DIFFRACTIONr_long_range_B_refined13.47263.61810062
X-RAY DIFFRACTIONr_long_range_B_other13.47263.61710062
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 54 -
Rwork0.258 1061 -
obs--98.07 %

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