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- PDB-3eqg: X-ray structure of the human mitogen-activated protein kinase kin... -

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Basic information

Entry
Database: PDB / ID: 3eqg
TitleX-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in a ternary complex with PD, ADP AND MG2P
ComponentsDual specificity mitogen-activated protein kinase kinase 1
KeywordsTRANSFERASE / MEK1 KINASE / ATP-binding / Disease mutation / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Tyrosine-protein kinase
Function / homology
Function and homology information


epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / placenta blood vessel development / regulation of axon regeneration / mitogen-activated protein kinase kinase / labyrinthine layer development / MAP-kinase scaffold activity / type B pancreatic cell proliferation / cerebellar cortex formation / Signaling by MAP2K mutants ...epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / placenta blood vessel development / regulation of axon regeneration / mitogen-activated protein kinase kinase / labyrinthine layer development / MAP-kinase scaffold activity / type B pancreatic cell proliferation / cerebellar cortex formation / Signaling by MAP2K mutants / regulation of Golgi inheritance / spindle pole body / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / positive regulation of axonogenesis / regulation of stress-activated MAPK cascade / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / protein kinase activator activity / MAPK3 (ERK1) activation / endodermal cell differentiation / face development / MAP kinase kinase activity / Bergmann glial cell differentiation / Uptake and function of anthrax toxins / thyroid gland development / Schwann cell development / keratinocyte differentiation / protein serine/threonine/tyrosine kinase activity / myelination / ERK1 and ERK2 cascade / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / insulin-like growth factor receptor signaling pathway / thymus development / Signal transduction by L1 / cell motility / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein serine/threonine kinase activity / 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 / chemotaxis / cellular senescence / Signaling by BRAF and RAF1 fusions / MAPK cascade / late endosome / heart development / scaffold protein binding / protein tyrosine kinase activity / positive regulation of ERK1 and ERK2 cascade / early endosome / protein kinase activity / negative regulation of cell population proliferation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / centrosome / positive regulation of gene expression / positive regulation of DNA-templated transcription / Golgi apparatus / endoplasmic reticulum / signal transduction / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / 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, ATP binding site ...: / 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, 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
Chem-4BM / ADENOSINE-5'-DIPHOSPHATE / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsFischmann, T.O.
CitationJournal: Biochemistry / Year: 2009
Title: Crystal Structures of MEK1 Binary and Ternary Complexes with Nucleotides and Inhibitors.
Authors: Fischmann, T.O. / Smith, C.K. / Mayhood, T.W. / Myers, J.E. / Reichert, P. / Mannarino, A. / Carr, D. / Zhu, H. / Wong, J. / Yang, R.S. / Le, H.V. / Madison, V.S.
History
DepositionSep 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)41,1106
Polymers40,1131
Non-polymers9975
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)82,22012
Polymers80,2262
Non-polymers1,99410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area2550 Å2
ΔGint-70 kcal/mol
Surface area28750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.000, 76.000, 222.320
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-5-

CA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dual specificity mitogen-activated protein kinase kinase 1 / MAP kinase kinase 1 / MAPKK 1 / ERK activator kinase 1 / MAPK/ERK kinase 1 / MEK1


Mass: 40113.215 Da / Num. of mol.: 1 / Fragment: Protein kinase domain, UNP residues 35-393 / Mutation: S265N, S266K, Y267F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1
References: UniProt: Q02750, mitogen-activated protein kinase kinase

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Non-polymers , 6 types, 49 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-4BM / N-{[(2R)-2,3-dihydroxypropyl]oxy}-3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]benzamide


Mass: 482.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14F3IN2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M TRIS-CL, pH 8.0; 18% PEG 4000; 0.2M CALCIUM CHLORIDE; 3% DMSO, VAPOR DIFFUSION HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13873 / % possible obs: 99.6 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.108 / Χ2: 1.002 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5411.30.4416770.9281100
2.54-2.5911.50.3536660.9551100
2.59-2.6411.40.3476710.9371100
2.64-2.6911.10.276841.1041100
2.69-2.7511.30.3156680.96199.9
2.75-2.8211.40.236710.9291100
2.82-2.8911.30.2316740.9351100
2.89-2.9611.20.1876810.9011100
2.96-3.0511.20.1646841.0021100
3.05-3.1511.20.146830.9641100
3.15-3.2611.20.1266820.9321100
3.26-3.3911.20.1026810.981100
3.39-3.5510.80.1076961.0671100
3.55-3.7310.70.0936961.0831100
3.73-3.9710.50.0996981.1641100
3.97-4.2710.50.0977041.1571100
4.27-4.710.50.17091.1431100
4.7-5.3810.40.0997241.0961100
5.38-6.7810.10.0917410.964199.9
6.78-508.50.0687830.837193.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
PDB_EXTRACT3.004data extraction
BUSTER-TNT2.1.1refinement
RefinementResolution: 2.5→16.54 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3
RfactorNum. reflection% reflectionSelection details
Rfree0.273 651 4.98 %RANDOM
Rwork0.207 ---
obs0.21 13725 94.03 %-
Displacement parametersBiso mean: 62.46 Å2
Baniso -1Baniso -2Baniso -3
1--14.006 Å20 Å20 Å2
2---14.006 Å20 Å2
3---28.013 Å2
Refinement stepCycle: LAST / Resolution: 2.5→16.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 56 44 2563
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01125672
X-RAY DIFFRACTIONt_angle_deg1.43134472
X-RAY DIFFRACTIONt_dihedral_angle_d25.5625410
X-RAY DIFFRACTIONIMPROPER ANGLES (DEGREES)63.90810
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01682
X-RAY DIFFRACTIONt_gen_planes0.0163625
X-RAY DIFFRACTIONt_it2.144256720
X-RAY DIFFRACTIONt_nbd0.044695
LS refinement shellResolution: 2.5→2.65 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.324 98 5.26 %
Rwork0.269 1766 -
all0.272 1864 -
obs--94.03 %

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