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- PDB-6yg6: Crystal structure of MKK7 (MAP2K7) covalently bound with type-II ... -

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Basic information

Entry
Database: PDB / ID: 6yg6
TitleCrystal structure of MKK7 (MAP2K7) covalently bound with type-II inhibitor TL10-105
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 / MAP kinase kinase activity / positive regulation of telomere maintenance / 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 / MAP kinase kinase activity / positive regulation of telomere maintenance / response to tumor necrosis factor / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 / stress-activated MAPK cascade / response to UV / 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
: / 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 domain profile. ...: / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-OQ8 / Dual specificity mitogen-activated protein kinase kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChaikuad, A. / Tan, L. / Wang, J. / Liang, Y. / Gray, N.S. / 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 / _citation_author.identifier_ORCID / _citation_author.name
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 23, 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
B: Dual specificity mitogen-activated protein kinase kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5018
Polymers69,9732
Non-polymers1,5286
Water2,936163
1
A: Dual specificity mitogen-activated protein kinase kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6883
Polymers34,9871
Non-polymers7022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity mitogen-activated protein kinase kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8135
Polymers34,9871
Non-polymers8264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.651, 69.934, 73.763
Angle α, β, γ (deg.)90.000, 119.360, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 120 - 419 / Label seq-ID: 6 - 305

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 34986.613 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-OQ8 / ~{N}-[4-[(4-ethylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl]-4-methyl-3-[2-[[(3~{S})-1-propanoylpyrrolidin-3-yl]amino]pyrimidin-4-yl]oxy-benzamide


Mass: 639.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40F3N7O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 19% PEG3350, 0.15 M ammonium acetate, 0.1 M tris, pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.15→47.33 Å / Num. obs: 35192 / % possible obs: 99.9 % / Redundancy: 5.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.05 / Rrim(I) all: 0.113 / Net I/av σ(I): 4.8 / Net I/σ(I): 10
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
2.15-2.275.10.9060.751170.6590.461.020.90699.9
2.27-2.45.30.611.148220.3020.6840.61100
2.4-2.575.40.3941.745310.1930.4410.394100
2.57-2.785.10.2522.742540.1270.2830.252100
2.78-3.045.40.1594.139170.0780.1780.159100
3.04-3.45.40.1036.235290.050.1150.103100
3.4-3.935.20.0649.331350.0320.0720.06499.9
3.93-4.815.50.05210.426490.0250.0580.05299.9
4.81-6.85.20.0531120770.0260.0590.05399.9
6.8-47.3295.10.0547.811610.0270.0610.05499.8

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dyl

2dyl


Resolution: 2.15→47.33 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 14.242 / SU ML: 0.181 / SU R Cruickshank DPI: 0.2578 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.198
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 1630 4.6 %RANDOM
Rwork0.2036 ---
obs0.2053 33542 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 164.97 Å2 / Biso mean: 62.631 Å2 / Biso min: 31.11 Å2
Baniso -1Baniso -2Baniso -3
1-3.82 Å20 Å23.1 Å2
2---4.17 Å20 Å2
3----1.92 Å2
Refinement stepCycle: final / Resolution: 2.15→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 108 163 4785
Biso mean--51.09 53.77 -
Num. residues----565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194748
X-RAY DIFFRACTIONr_bond_other_d0.0050.024636
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.976393
X-RAY DIFFRACTIONr_angle_other_deg1.016310700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05123.981206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62215874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5491530
X-RAY DIFFRACTIONr_chiral_restr0.0780.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215428
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021042
Refine LS restraints NCS

Ens-ID: 1 / Number: 34370 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 128 -
Rwork0.285 2452 -
all-2580 -
obs--99.85 %
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)
13.8801-0.92-2.57012.80971.32036.9070.0081-0.63160.08990.448-0.0040.08870.2275-0.0725-0.00410.2048-0.0529-0.03570.21790.0590.1214-7.3528-16.774321.1578
21.76230.6187-0.62464.2586-0.31852.32540.0074-0.2777-0.02760.1608-0.006-0.1107-0.12850.0035-0.00130.05980.0032-0.01130.05040.00340.0044-2.79996.106811.4261
34.40241.76751.2077.2011-0.89488.5157-0.04050.7321-0.1925-0.7985-0.0981-0.09010.54530.08750.13870.28780.10730.06570.3191-0.00380.186-28.138-16.462-15.8198
411.0734-5.3576-0.35476.2624-4.43285.9906-0.3390.06691.1790.27420.2361-0.5354-0.15280.06360.1030.79910.0020.03680.8970.01620.601-20.3283-3.0233-30.8739
51.5988-1.5733-1.37145.85830.47163.0348-0.01090.2448-0.2356-0.4786-0.2759-0.16950.21960.32330.28680.15940.0739-0.0340.296-0.02840.1553-32.09162.4179-13.7031
66.05423.1787-8.82821.7386-4.685812.91590.08640.0797-0.07540.0118-0.1729-0.0449-0.15710.05230.08650.6253-0.0661-0.05130.68970.01690.5473-23.972121.4948-22.8429
73.60090.2333-0.88842.9551-1.36544.22070.10270.2348-0.0347-0.1459-0.11330.0254-0.19120.03760.01060.08450.0616-0.02170.1185-0.05640.0966-41.582114.944-11.0478
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A119 - 181
2X-RAY DIFFRACTION2A182 - 419
3X-RAY DIFFRACTION3B120 - 167
4X-RAY DIFFRACTION4B168 - 178
5X-RAY DIFFRACTION5B179 - 307
6X-RAY DIFFRACTION6B308 - 318
7X-RAY DIFFRACTION7B319 - 419

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