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

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Basic information

Entry
Database: PDB / ID: 5twu
TitleStructure of Maternal Embryonic Leucine Zipper Kinase
ComponentsMaternal embryonic leucine zipper kinaseMELK
KeywordsTRANSFERASE / kinase inhibitor / basal-like breast cancer
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 / apoptotic process / lipid binding / 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
Maternal embryonic leucine zipper kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.603 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 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: 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 1.2Oct 4, 2023Group: 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: Maternal embryonic leucine zipper kinase
B: Maternal embryonic leucine zipper kinase


Theoretical massNumber of molelcules
Total (without water)79,3142
Polymers79,3142
Non-polymers00
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-16 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.126, 78.599, 79.110
Angle α, β, γ (deg.)90.000, 110.600, 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 / Fragment: UNP residues 1-340
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
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: 2.6→50 Å / Num. obs: 22978 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 54.06 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.167 / Net I/av σ(I): 16.909 / Net I/σ(I): 15.2 / Num. measured all: 85366
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.6-2.693.80.6321100
2.69-2.83.80.4431100
2.8-2.933.80.331100
2.93-3.083.80.2091100
3.08-3.283.80.141100
3.28-3.533.80.0951100
3.53-3.883.70.0651100
3.88-4.453.60.0521100
4.45-5.63.50.053199.5
5.6-503.50.033198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BL1

4bl1


Resolution: 2.603→48.171 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.69
RfactorNum. reflection% reflection
Rfree0.2346 1985 8.65 %
Rwork0.1607 --
obs0.1672 22950 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.77 Å2 / Biso mean: 62.11 Å2 / Biso min: 23.08 Å2
Refinement stepCycle: final / Resolution: 2.603→48.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5151 0 0 332 5483
Biso mean---66.47 -
Num. residues----633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085269
X-RAY DIFFRACTIONf_angle_d1.1567112
X-RAY DIFFRACTIONf_chiral_restr0.046788
X-RAY DIFFRACTIONf_plane_restr0.006888
X-RAY DIFFRACTIONf_dihedral_angle_d14.5051987
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2945X-RAY DIFFRACTION5.799TORSIONAL
12B2945X-RAY DIFFRACTION5.799TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6032-2.66830.32581330.22331437157098
2.6683-2.74040.2951410.216314941635100
2.7404-2.8210.34191420.212615101652100
2.821-2.91210.29581500.207514931643100
2.9121-3.01610.30111350.194114891624100
3.0161-3.13690.28411530.184714801633100
3.1369-3.27960.32961360.189415201656100
3.2796-3.45250.26971390.171414881627100
3.4525-3.66870.21761430.158814831626100
3.6687-3.95190.21771500.136515271677100
3.9519-4.34930.19861400.121714981638100
4.3493-4.97810.20351350.12441505164099
4.9781-6.26970.21751460.165915071653100
6.2697-48.1790.19391420.1671534167698
Refinement TLS params.Method: refined / Origin x: 13.0412 Å / Origin y: -9.0966 Å / Origin z: 41.8165 Å
111213212223313233
T0.2988 Å20.0289 Å2-0.0232 Å2-0.1918 Å20.0243 Å2--0.4231 Å2
L0.8912 °20.1341 °20.8612 °2-0.288 °20.459 °2--5.0737 °2
S0.0646 Å °0.0033 Å °-0.1294 Å °0.0714 Å °0.0193 Å °-0.0773 Å °0.2948 Å °0.2573 Å °-0.0726 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-2 - 333
2X-RAY DIFFRACTION1allB-3 - 335
3X-RAY DIFFRACTION1allZ1 - 360

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