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- PDB-6yg5: Crystal structure of MKK7 (MAP2K7) in complex with ASC69 -

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Basic information

Entry
Database: PDB / ID: 6yg5
TitleCrystal structure of MKK7 (MAP2K7) in complex with ASC69
ComponentsDual specificity mitogen-activated protein kinase kinase 7
KeywordsTRANSFERASE / kinase / kinase inhibitor / MKK7 / MEK7 / MAP2K7 / MAP2K / MEK / JNK signaling / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere maintenance / MAP kinase kinase activity / response to tumor necrosis factor / Uptake and function of anthrax toxins / MAP kinase activity ...JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere maintenance / MAP kinase kinase activity / response to tumor necrosis factor / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 / response to UV / stress-activated MAPK cascade / JNK cascade / molecular function activator activity / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of JNK cascade / FCERI mediated MAPK activation / response to wounding / cellular senescence / cellular response to lipopolysaccharide / response to heat / protein tyrosine kinase activity / protein phosphatase binding / Oxidative Stress Induced Senescence / positive regulation of ERK1 and ERK2 cascade / protein serine kinase activity / apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / magnesium ion binding / signal transduction / ATP binding / nucleus / cytoplasm / cytosol
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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-IHH / Dual specificity mitogen-activated protein kinase kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell Chem Biol / Year: 2020
Title: Catalytic Domain Plasticity of MKK7 Reveals Structural Mechanisms of Allosteric Activation and Diverse Targeting Opportunities.
Authors: Schroder, M. / Tan, L. / Wang, J. / Liang, Y. / Gray, N.S. / Knapp, S. / Chaikuad, A.
History
DepositionMar 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3582
Polymers34,9771
Non-polymers3811
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.660, 68.031, 84.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dual specificity mitogen-activated protein kinase kinase 7 / MAPKK 7 / JNK-activating kinase 2 / MAPK/ERK kinase 7 / MEK 7 / Stress-activated protein kinase ...MAPKK 7 / JNK-activating kinase 2 / MAPK/ERK kinase 7 / MEK 7 / Stress-activated protein kinase kinase 4 / SAPKK4 / c-Jun N-terminal kinase kinase 2 / JNKK 2


Mass: 34976.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K7, JNKK2, MEK7, MKK7, PRKMK7, SKK4 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: O14733, mitogen-activated protein kinase kinase
#2: Chemical ChemComp-IHH / [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]quinazolin-2-yl}amino)phenyl]acetonitrile


Mass: 381.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19N7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 16% PEG3350, 0.2 M ammonium acetate, 0.1 M tris, pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→39.64 Å / Num. obs: 13948 / % possible obs: 99.5 % / Redundancy: 4.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.031 / Rrim(I) all: 0.069 / Net I/av σ(I): 5.2 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.4-2.534.70.73120130.7660.3640.8190.7399.6
2.53-2.684.80.4241.818600.2090.4740.42499.4
2.68-2.874.80.2592.817920.1280.290.25999.3
2.87-3.14.70.1474.916750.0740.1650.14799.7
3.1-3.394.70.0927.515290.0470.1030.09299.3
3.39-3.794.80.0599.914020.030.0660.05999.6
3.79-4.384.80.0512.112500.0250.0560.0599.8
4.38-5.374.50.04811.410810.0250.0550.04899.5
5.37-7.594.40.04910.98460.0250.0560.04999.5
7.59-39.644.10.04810.45000.0260.0550.04898.1

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dyl

2dyl


Resolution: 2.4→39.64 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 26.373 / SU ML: 0.271 / SU R Cruickshank DPI: 0.3716 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.372 / ESU R Free: 0.274
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2815 677 4.9 %RANDOM
Rwork0.2307 ---
obs0.2333 13237 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 141 Å2 / Biso mean: 77.071 Å2 / Biso min: 52.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å2-0 Å2-0 Å2
2---2.12 Å20 Å2
3---2.99 Å2
Refinement stepCycle: final / Resolution: 2.4→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 26 13 2099
Biso mean--100.34 72.27 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132128
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171991
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.6432867
X-RAY DIFFRACTIONr_angle_other_deg1.1231.5944614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1165259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71322.816103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91815380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.971511
X-RAY DIFFRACTIONr_chiral_restr0.0420.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022451
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02438
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 36 -
Rwork0.314 972 -
all-1008 -
obs--99.7 %
Refinement TLS params.Method: refined / Origin x: 18.103 Å / Origin y: 9.201 Å / Origin z: 11.928 Å
111213212223313233
T0.4477 Å2-0.1033 Å2-0.0342 Å2-0.6607 Å20.0684 Å2--0.0421 Å2
L2.7373 °2-2.0765 °2-0.8219 °2-1.5919 °20.6437 °2--1.0831 °2
S0.0153 Å °-0.0865 Å °-0.2117 Å °0.0499 Å °0.0546 Å °0.1568 Å °0.2001 Å °-0.019 Å °-0.0699 Å °

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