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- PDB-5tx3: Structure of Maternal Embryonic Leucine Zipper Kinase -

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Basic information

Entry
Database: PDB / ID: 5tx3
TitleStructure of Maternal Embryonic Leucine Zipper Kinase
ComponentsMaternal embryonic leucine zipper kinaseMELK
KeywordsTransferase/Transferase Inhibitor / kinase inhibitor / 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-7MY / Maternal embryonic leucine zipper kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLi, Q. / Seo, H.-S. / Huang, H.-T. / Gray, N.S. / Dhe-Paganon, S. / Eck, M.J.
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 15, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Maternal embryonic leucine zipper kinase
B: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2534
Polymers79,3142
Non-polymers9392
Water86548
1
A: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1272
Polymers39,6571
Non-polymers4701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1272
Polymers39,6571
Non-polymers4701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.620, 78.670, 78.960
Angle α, β, γ (deg.)90.000, 110.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 0 / Label seq-ID: 4

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and segidAA
2chain B and segidBB

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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: 39656.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MELK, KIAA0175 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q14680, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-7MY / 7-[(1S)-4-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-2-({3-[(pyrrolidin-1-yl)methyl]phenyl}amino)-5,7-dihydro-6H-pyrrolo[2,3-d]pyrimidin-6-one


Mass: 469.578 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H31N5O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→47.901 Å / Num. obs: 16392 / % possible obs: 99.05 % / Observed criterion σ(F): 1.37 / Redundancy: 4 % / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.901 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.38
RfactorNum. reflection% reflection
Rfree0.2528 1639 10 %
Rwork0.1818 --
obs0.1891 16392 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 276.73 Å2 / Biso mean: 88.09 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.9→47.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4961 0 70 48 5079
Biso mean--60.36 78.93 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095147
X-RAY DIFFRACTIONf_angle_d1.3046957
X-RAY DIFFRACTIONf_chiral_restr0.051761
X-RAY DIFFRACTIONf_plane_restr0.006858
X-RAY DIFFRACTIONf_dihedral_angle_d15.6011924
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2849X-RAY DIFFRACTION8.887TORSIONAL
12B2849X-RAY DIFFRACTION8.887TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9001-2.98540.30771270.2281227135499
2.9854-3.08170.29641490.22261216136599
3.0817-3.19190.33731260.21781212133899
3.1919-3.31960.29311440.19831207135199
3.3196-3.47070.29971300.18971244137499
3.4707-3.65360.29531350.191612231358100
3.6536-3.88240.2551380.171212361374100
3.8824-4.1820.25481370.1621240137799
4.182-4.60260.20441420.14851232137499
4.6026-5.26780.2581310.16321235136699
5.2678-6.63410.25921380.20381239137799
6.6341-47.90770.2111420.1871242138497
Refinement TLS params.Method: refined / Origin x: 13.1774 Å / Origin y: -8.6491 Å / Origin z: 41.9215 Å
111213212223313233
T0.4579 Å20.0305 Å2-0.1082 Å2-0.3383 Å20.0155 Å2--0.5322 Å2
L1.5758 °2-0.0679 °21.3251 °2-1.0851 °20.0014 °2--5.5225 °2
S-0.1932 Å °-0.0822 Å °0.0474 Å °0.2672 Å °0.0438 Å °-0.1952 Å °0.0065 Å °0.3816 Å °0.1331 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-2 - 333
2X-RAY DIFFRACTION1allA1000
3X-RAY DIFFRACTION1allB-2 - 334
4X-RAY DIFFRACTION1allB1001
5X-RAY DIFFRACTION1allC1 - 66
6X-RAY DIFFRACTION1allC68 - 97

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