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- PDB-5twl: Structure of Maternal Embryonic Leucine Zipper Kinase -

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Basic information

Entry
Database: PDB / ID: 5twl
TitleStructure of Maternal Embryonic Leucine Zipper Kinase
ComponentsMaternal embryonic leucine zipper kinaseMELK
KeywordsTransferase/Transferase Inhibitor / kinase inhibitor / basal-like breast cancer / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G2/M transition of mitotic cell cycle / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase ...neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G2/M transition of mitotic cell cycle / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / apoptotic process / calcium ion binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Maternal embryonic leucine zipper kinase, catalytic domain / : / Maternal embryonic leucine zipper kinase, UBA domain / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Maternal embryonic leucine zipper kinase, catalytic domain / : / Maternal embryonic leucine zipper kinase, UBA domain / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / 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
Similarity search - Domain/homology
Chem-H91 / Maternal embryonic leucine zipper kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.42 Å
AuthorsSeo, H.-S. / Huang, H.-T. / Gray, N.S. / Dhe-Paganon, S.
CitationJournal: Elife / Year: 2017
Title: MELK is not necessary for the proliferation of basal-like breast cancer cells.
Authors: Huang, H.T. / Seo, H.S. / Zhang, T. / Wang, Y. / Jiang, B. / Li, Q. / Buckley, D.L. / Nabet, B. / Roberts, J.M. / Paulk, J. / Dastjerdi, S. / Winter, G.E. / McLauchlan, H. / Moran, J. / ...Authors: Huang, H.T. / Seo, H.S. / Zhang, T. / Wang, Y. / Jiang, B. / Li, Q. / Buckley, D.L. / Nabet, B. / Roberts, J.M. / Paulk, J. / Dastjerdi, S. / Winter, G.E. / McLauchlan, H. / Moran, J. / Bradner, J.E. / Eck, M.J. / Dhe-Paganon, S. / Zhao, J.J. / Gray, N.S.
History
DepositionNov 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8812
Polymers39,3821
Non-polymers4991
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.520, 68.300, 104.950
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 Maternal embryonic leucine zipper kinase / MELK / hMELK / Protein kinase Eg3 / pEg3 kinase / Protein kinase PK38 / hPK38 / Tyrosine-protein kinase MELK


Mass: 39381.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MELK, KIAA0175 / Production host: Escherichia coli (E. coli)
References: UniProt: Q14680, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-H91 / 9-(3,5-dichloro-4-hydroxyphenyl)-1-{trans-4-[(dimethylamino)methyl]cyclohexyl}-3,4-dihydropyrimido[5,4-c]quinolin-2(1H)-one


Mass: 499.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28Cl2N4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: magnesium chloride, PEG 3350, BIS-TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.42→38.77 Å / Num. obs: 15943 / % possible obs: 97.47 % / Redundancy: 4.1 % / Net I/σ(I): 12.52

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata processing
PDB_EXTRACT3.2data extraction
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→38.767 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.38
RfactorNum. reflection% reflection
Rfree0.2491 815 5.11 %
Rwork0.1956 --
obs0.1983 15941 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.36 Å2 / Biso mean: 59.2616 Å2 / Biso min: 28.43 Å2
Refinement stepCycle: final / Resolution: 2.42→38.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 34 36 2600
Biso mean--50.58 51.8 -
Num. residues----319
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)
18.8665-1.3911-0.02827.39680.1584.857-0.0748-0.57010.75960.2066-0.11250.47220.0357-0.22340.24310.3942-0.06740.0890.4657-0.15490.43-14.45669.60585.7413
26.61820.6408-2.24210.68791.26042.014-0.04380.19690.5925-0.0516-0.0760.19150.0571-0.10260.11680.4441-0.0198-0.03620.38420.05070.4582-8.19887.3343-6.2091
36.9050.3626-1.85273.2533-0.36322.846-0.3838-0.2758-0.14370.17380.1885-0.08320.30420.22940.18810.43660.03760.01190.2913-0.02320.30383.01481.341-11.9788
44.65953.0971-3.91153.2662-0.59176.1598-0.09321.08490.2326-0.83090.35860.62-0.0624-1.2307-0.26740.58280.0504-0.09380.57210.08310.5318-3.657910.3829-23.9887
53.6701-1.0133-0.20824.5789-1.01173.4016-0.19530.4375-0.0783-0.39720.1316-0.32060.10670.06940.05610.3635-0.00170.05390.3746-0.03240.306510.64116.4298-24.0275
64.53952.3559-4.9831.3081-1.09857.91330.3837-0.1353-0.30120.1744-0.30910.060.599-0.49640.06570.8453-0.1062-0.05610.51440.11920.7883-10.6376-13.01010.0735
75.67781.8836-0.09797.1618-2.96735.2170.5078-0.8127-0.7919-0.3183-0.4105-0.20630.6556-0.5234-0.11040.5779-0.12160.00080.43450.04680.5174-14.7569-9.02424.26
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 35 )A0 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 105 )A36 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 148 )A106 - 148
4X-RAY DIFFRACTION4chain 'A' and (resid 149 through 186 )A149 - 186
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 269 )A187 - 269
6X-RAY DIFFRACTION6chain 'A' and (resid 270 through 297 )A270 - 297
7X-RAY DIFFRACTION7chain 'A' and (resid 298 through 333 )A298 - 333

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