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- PDB-2qnj: Kinase and Ubiquitin-associated domains of MARK3/Par-1 -

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Basic information

Entry
Database: PDB / ID: 2qnj
TitleKinase and Ubiquitin-associated domains of MARK3/Par-1
ComponentsMAP/microtubule affinity-regulating kinase 3
KeywordsTRANSFERASE / serine/threonine protein kinase / ubiquitin-associated domain / MARK / PAR-1
Function / homology
Function and homology information


negative regulation of protein localization to nucleus / tau-protein kinase activity / negative regulation of hippo signaling / regulation of G2/M transition of mitotic cell cycle / Transcriptional and post-translational regulation of MITF-M expression and activity / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / tau protein binding / Negative regulation of MAPK pathway ...negative regulation of protein localization to nucleus / tau-protein kinase activity / negative regulation of hippo signaling / regulation of G2/M transition of mitotic cell cycle / Transcriptional and post-translational regulation of MITF-M expression and activity / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / tau protein binding / Negative regulation of MAPK pathway / microtubule cytoskeleton organization / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / protein phosphatase binding / protein phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / extracellular exosome / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. ...: / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Helicase, Ruva Protein; domain 3 / 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, ATP binding site / Protein kinases ATP-binding region signature. / 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
MAP/microtubule affinity-regulating kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsMurphy, J.M. / Ceccarelli, D.F.J. / Sicheri, F. / Pawson, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Conformational instability of the MARK3 UBA domain compromises ubiquitin recognition and promotes interaction with the adjacent kinase domain
Authors: Murphy, J.M. / Korzhnev, D.M. / Ceccarelli, D.F. / Briant, D.J. / Zarrine-Afsar, A. / Sicheri, F. / Kay, L.E. / Pawson, T.
History
DepositionJul 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAP/microtubule affinity-regulating kinase 3
B: MAP/microtubule affinity-regulating kinase 3


Theoretical massNumber of molelcules
Total (without water)75,3372
Polymers75,3372
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.675, 112.544, 117.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MAP/microtubule affinity-regulating kinase 3 / Cdc25C- associated protein kinase 1 / cTAK1 / C-TAK1 / Serine/threonine protein kinase p78 / ...Cdc25C- associated protein kinase 1 / cTAK1 / C-TAK1 / Serine/threonine protein kinase p78 / Ser/Thr protein kinase PAR-1 / Protein kinase STK10


Mass: 37668.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MARK3, CTAK1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3
References: UniProt: P27448, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M LiSO4, 100 mM HEPES pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97899 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 1, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.69→30 Å / Num. all: 23737 / Num. obs: 23590 / % possible obs: 99.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.6
Reflection shellResolution: 2.69→2.8 Å / Redundancy: 6 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 3.3 / % possible all: 95.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.69 Å39.43 Å
Translation2.69 Å39.43 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZMU

1zmu


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.88 / SU B: 27.927 / SU ML: 0.271 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.967 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27926 1209 5.2 %RANDOM
Rwork0.21543 ---
obs0.21859 22204 99.94 %-
all-23590 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.715 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å20 Å2
2--0.31 Å20 Å2
3----2.86 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5028 0 0 47 5075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225122
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9756918
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44123.983231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.69615909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5321534
X-RAY DIFFRACTIONr_chiral_restr0.10.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023831
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.22299
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.23511
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3670.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4370.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6381.53264
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04125090
X-RAY DIFFRACTIONr_scbond_it1.6432097
X-RAY DIFFRACTIONr_scangle_it2.6094.51828
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 79 -
Rwork0.312 1612 -
obs--99.53 %
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)
10.8892-0.34830.70471.2797-1.42532.23650.0206-0.0440.00820.0218-0.0124-0.07910.12720.04-0.00820.00740.02070.0222-0.0665-0.053-0.017818.57325.99422.613
21.3091.00821.03782.18021.4621.8341-0.08970.06730.0823-0.067-0.00430.0191-0.11830.18610.094-0.047-0.00560.0263-0.00460.0512-0.04828.7439.84867.876
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA43 - 3661 - 324
2X-RAY DIFFRACTION2BB43 - 3661 - 324

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