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- PDB-4lqq: Crystal structure of the Cbk1(T743E)-Mob2 kinase-coactivator comp... -

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Basic information

Entry
Database: PDB / ID: 4lqq
TitleCrystal structure of the Cbk1(T743E)-Mob2 kinase-coactivator complex in crystal form B
Components
  • CBK1 kinase activator protein MOB2
  • Serine/threonine-protein kinase CBK1
KeywordsTRANSFERASE/TRANSFERASE activator / Kinase / TRANSFERASE-TRANSFERASE activator complex
Function / homology
Function and homology information


budding cell apical bud growth / regulation of fungal-type cell wall organization / cellular bud / establishment or maintenance of actin cytoskeleton polarity / prospore membrane / incipient cellular bud site / septum digestion after cytokinesis / cellular bud tip / cellular bud neck / serine/threonine protein kinase complex ...budding cell apical bud growth / regulation of fungal-type cell wall organization / cellular bud / establishment or maintenance of actin cytoskeleton polarity / prospore membrane / incipient cellular bud site / septum digestion after cytokinesis / cellular bud tip / cellular bud neck / serine/threonine protein kinase complex / mating projection tip / regulation of protein secretion / establishment or maintenance of cell polarity / protein kinase activator activity / cytoplasmic stress granule / cell cortex / non-specific serine/threonine protein kinase / intracellular signal transduction / cell division / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / : / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. ...MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / : / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / CBK1 kinase activator protein MOB2 / Serine/threonine-protein kinase CBK1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsGogl, G. / Remenyi, A.
CitationJournal: Plos Biol. / Year: 2015
Title: The Structure of an NDR/LATS Kinase-Mob Complex Reveals a Novel Kinase-Coactivator System and Substrate Docking Mechanism.
Authors: Gogl, G. / Schneider, K.D. / Yeh, B.J. / Alam, N. / Nguyen Ba, A.N. / Moses, A.M. / Hetenyi, C. / Remenyi, A. / Weiss, E.L.
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase CBK1
B: CBK1 kinase activator protein MOB2
D: Serine/threonine-protein kinase CBK1
E: CBK1 kinase activator protein MOB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,9065
Polymers174,4004
Non-polymers5061
Water00
1
A: Serine/threonine-protein kinase CBK1
B: CBK1 kinase activator protein MOB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7063
Polymers87,2002
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-12 kcal/mol
Surface area31090 Å2
MethodPISA
2
D: Serine/threonine-protein kinase CBK1
E: CBK1 kinase activator protein MOB2


Theoretical massNumber of molelcules
Total (without water)87,2002
Polymers87,2002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-8 kcal/mol
Surface area29020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.740, 139.060, 187.580
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serine/threonine-protein kinase CBK1 / Cell wall biosynthesis kinase


Mass: 58784.582 Da / Num. of mol.: 2 / Fragment: UNP residues 251-756 / Mutation: T743E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CBK1, N1727, YNL161W / Production host: Escherichia coli (E. coli)
References: UniProt: P53894, non-specific serine/threonine protein kinase
#2: Protein CBK1 kinase activator protein MOB2 / MPS1 binder 2 / Maintenance of ploidy protein MOB2


Mass: 28415.197 Da / Num. of mol.: 2 / Fragment: UNP residues 46-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MOB2, YFL034C-B, YFL035C, YFL035C-A / Production host: Escherichia coli (E. coli) / References: UniProt: P43563
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 296 K / Method: microbatch under oil / pH: 5.5
Details: four fold excess pepSSD1, 25% PEG 20,000 buffered with 0.1M Na-citrate, pH 5.5, Microbatch under oil, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 28, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.49
ReflectionResolution: 3.6→46.49 Å / Num. all: 23820 / Num. obs: 23529 / % possible obs: 98.8 % / Observed criterion σ(F): 1.36 / Observed criterion σ(I): 1.36
Reflection shellResolution: 3.6→3.69 Å / % possible all: 91.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→46.49 Å / σ(F): 1.36 / Phase error: 36.23 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3194 1217 5.17 %
Rwork0.258 --
obs0.2621 23527 98.82 %
all-23820 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7467 0 31 0 7498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017688
X-RAY DIFFRACTIONf_angle_d1.82610494
X-RAY DIFFRACTIONf_dihedral_angle_d20.5372584
X-RAY DIFFRACTIONf_chiral_restr0.131175
X-RAY DIFFRACTIONf_plane_restr0.0071353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.74740.42131190.38172314X-RAY DIFFRACTION88
3.7474-3.91760.32881390.27742507X-RAY DIFFRACTION95
3.9176-4.12370.32591240.29612452X-RAY DIFFRACTION95
4.1237-4.38140.35231310.28012484X-RAY DIFFRACTION95
4.3814-4.71870.36271350.27562531X-RAY DIFFRACTION95
4.7187-5.19160.33851280.2692454X-RAY DIFFRACTION95
5.1916-5.93840.30921350.26442475X-RAY DIFFRACTION95
5.9384-7.46490.33121320.2562533X-RAY DIFFRACTION95
7.4649-31.26450.27891640.20722493X-RAY DIFFRACTION93

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