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- PDB-6yg1: Crystal structure of MKK7 (MAP2K7) in an active state, allosteric... -

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Basic information

Entry
Database: PDB / ID: 6yg1
TitleCrystal structure of MKK7 (MAP2K7) in an active state, allosterically triggered by the N-terminal helix
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 / Scottish Structural Proteomics Facility / SSPF
Function / homology
Function and homology information


regulation of motor neuron apoptotic process / JUN kinase kinase activity / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / positive regulation of telomere maintenance / Uptake and function of anthrax toxins / response to tumor necrosis factor / cellular response to interleukin-1 ...regulation of motor neuron apoptotic process / JUN kinase kinase activity / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / positive regulation of telomere maintenance / Uptake and function of anthrax toxins / response to tumor necrosis factor / cellular response to interleukin-1 / MAP kinase activity / response to UV / stress-activated MAPK cascade / positive regulation of JUN kinase activity / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / molecular function activator activity / positive regulation of JNK cascade / FCERI mediated MAPK activation / response to wounding / cellular senescence / response to heat / cellular response to lipopolysaccharide / protein phosphatase binding / Oxidative Stress Induced Senescence / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / 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 / cytosol / cytoplasm
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
Dual specificity mitogen-activated protein kinase kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsChaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC) / Scottish Structural Proteomics Facility (SSPF)
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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
C: Dual specificity mitogen-activated protein kinase kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,40930
Polymers118,8903
Non-polymers1,52027
Water4,630257
1
A: Dual specificity mitogen-activated protein kinase kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,70819
Polymers39,6301
Non-polymers1,07818
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)39,9637
Polymers39,6301
Non-polymers3336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity mitogen-activated protein kinase kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7384
Polymers39,6301
Non-polymers1083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.160, 67.870, 142.780
Angle α, β, γ (deg.)90.000, 114.760, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA109 - 41936 - 346
21ASPASPBB109 - 41936 - 346
12SERSERAA102 - 41929 - 346
22SERSERCC102 - 41929 - 346
13ASPASPBB109 - 41936 - 346
23ASPASPCC109 - 41936 - 346

NCS ensembles :
ID
1
2
3

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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: 39629.953 Da / Num. of mol.: 3
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 27% PEG3350, 0.2 M potassium thiocyanate, 10% ethylene glycol, 0.1 M bis-tris propane, pH 7.5

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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: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.22→64.83 Å / Num. obs: 54756 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.053 / Rrim(I) all: 0.105 / Net I/av σ(I): 5.5 / Net I/σ(I): 8.2
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
2.22-2.343.50.6611.179700.6750.4060.7790.66199.8
2.34-2.483.90.4821.575470.2740.5560.48299.9
2.48-2.653.70.3092.370550.180.3590.30999.9
2.65-2.873.50.2033.665890.1240.2390.20399.9
2.87-3.143.90.1395.160670.0790.160.13999.9
3.14-3.513.80.0937.255350.0550.1090.09399.9
3.51-4.053.70.0688.948650.040.080.06899.7
4.05-4.963.80.0619.740990.0350.0710.06199.4
4.96-7.023.60.0649.432170.0380.0750.06499.6
7.02-58.5113.50.0510.718120.030.0590.0599.4

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dyl

2dyl


Resolution: 2.22→64.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 14.172 / SU ML: 0.173 / SU R Cruickshank DPI: 0.2771 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.201
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 2724 5 %RANDOM
Rwork0.2037 ---
obs0.2051 52028 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 161.19 Å2 / Biso mean: 63.77 Å2 / Biso min: 19.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å2-0 Å2-0.91 Å2
2--2.88 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 2.22→64.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7318 0 96 257 7671
Biso mean--64.89 50.87 -
Num. residues----936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197562
X-RAY DIFFRACTIONr_bond_other_d0.0070.027340
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.98110160
X-RAY DIFFRACTIONr_angle_other_deg1.183316923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9985940
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2424.18323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.536151368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2581546
X-RAY DIFFRACTIONr_chiral_restr0.0890.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218364
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021620
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A363920.06
12B363920.06
21A371220.07
22C371220.07
31B354640.07
32C354640.07
LS refinement shellResolution: 2.22→2.278 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 197 -
Rwork0.299 3826 -
all-4023 -
obs--99.68 %
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)
16.18273.18272.56756.38482.47275.79070.19850.0649-0.1280.37370.0006-0.9901-0.28280.8953-0.19910.1580.0173-0.09580.32730.0640.333251.0956-14.406712.1886
21.92960.67590.11333.2355-1.00322.2118-0.0325-0.2165-0.2130.171-0.0485-0.33220.21460.13190.0810.05410.0287-0.01140.03750.02190.045645.44548.84024.0031
312.5275-1.0559-0.07520.92090.33481.49860.124-0.691-0.18650.3287-0.0263-0.4907-0.09920.2048-0.09770.62330.1168-0.03530.60630.17420.40026.4863-12.188955.1675
42.291-0.2708-0.44862.51650.30845.2188-0.1753-0.8806-0.08740.72610.151-0.3332-0.23130.05780.02430.33120.12-0.07550.4239-0.0320.216813.9347-5.799739.8762
55.4811-1.2776-0.28352.5695-0.15833.4219-0.0816-0.42550.34370.24630.0101-0.1188-0.30090.06650.07150.1280.0079-0.05390.0392-0.03060.042119.9897-5.426724.4695
63.88790.85031.93512.6814-3.832610.0655-0.0471-0.45190.19970.0990.09580.23820.0231-0.8679-0.04870.60450.04680.03920.8858-0.04720.738815.707-42.941147.9669
71.82160.1291-0.24122.2071-1.16054.8216-0.13080.1143-0.0369-0.01-0.18930.04160.27540.16690.320.16360.0833-0.01160.25580.05950.089938.8156-35.357941.0213
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A102 - 169
2X-RAY DIFFRACTION2A170 - 420
3X-RAY DIFFRACTION3B102 - 175
4X-RAY DIFFRACTION4B176 - 296
5X-RAY DIFFRACTION5B297 - 420
6X-RAY DIFFRACTION6C102 - 179
7X-RAY DIFFRACTION7C180 - 421

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