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- PDB-5ncl: Crystal structure of the Cbk1-Mob2 kinase-coactivator complex wit... -

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Basic information

Entry
Database: PDB / ID: 5ncl
TitleCrystal structure of the Cbk1-Mob2 kinase-coactivator complex with an SSD1 peptide
Components
  • CBK1 kinase activator protein MOB2
  • Protein SSD1
  • Serine/threonine-protein kinase CBK1
KeywordsSIGNALING PROTEIN / kinase
Function / homology
Function and homology information


budding cell apical bud growth / regulation of fungal-type cell wall organization / cellular bud / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / incipient cellular bud site / septum digestion after cytokinesis / cellular bud tip / serine/threonine protein kinase complex / intracellular mRNA localization ...budding cell apical bud growth / regulation of fungal-type cell wall organization / cellular bud / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / incipient cellular bud site / septum digestion after cytokinesis / cellular bud tip / serine/threonine protein kinase complex / intracellular mRNA localization / cellular bud neck / mating projection tip / regulation of G1 to G0 transition / establishment or maintenance of cell polarity / regulation of protein secretion / mRNA catabolic process / protein kinase activator activity / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / P-body / mRNA 5'-UTR binding / cytoplasmic stress granule / 3'-5'-RNA exonuclease activity / cell cortex / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / negative regulation of translation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / mRNA binding / signal transduction / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
DIS3-like exonuclease 2, C-terminal / DIS3-like exonuclease 2 C terminal / MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site ...DIS3-like exonuclease 2, C-terminal / DIS3-like exonuclease 2 C terminal / MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / : / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Nucleic acid-binding, OB-fold / 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 / Protein SSD1 / 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: 3.15 Å
AuthorsGogl, G. / Remenyi, A. / Parker, B. / Weiss, E.
CitationJournal: Biochemistry / Year: 2020
Title: Ndr/Lats Kinases Bind Specific Mob-Family Coactivators through a Conserved and Modular Interface.
Authors: Parker, B.W. / Gogl, G. / Balint, M. / Hetenyi, C. / Remenyi, A. / Weiss, E.L.
History
DepositionMar 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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
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: Serine/threonine-protein kinase CBK1
B: CBK1 kinase activator protein MOB2
D: Protein SSD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8784
Polymers88,3723
Non-polymers5061
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-25 kcal/mol
Surface area30820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.430, 79.990, 117.590
Angle α, β, γ (deg.)90.00, 117.60, 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: 58756.566 Da / Num. of mol.: 1 / Fragment: UNP Residues 251-756
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CBK1, YNL161W, N1727 / 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.: 1 / Fragment: UNP Residues 46-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MOB2, YFL034C-B, YFL035C, YFL035C-A / Production host: Escherichia coli (E. coli) / References: UniProt: P43563
#3: Protein/peptide Protein SSD1 / Protein SRK1


Mass: 1200.273 Da / Num. of mol.: 1 / Fragment: UNP Residues 205-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SSD1, CLA1, RLD1, SRK1, YDR293C, D9819.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P24276
#4: 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: 4.06 Å3/Da / Density % sol: 69.7 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 5.5 / Details: 25% PEG 20,000 BUFFERED WITH 0.1M NA-CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→44.595 Å / Num. obs: 19888 / % possible obs: 99.7 % / Redundancy: 7.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.168 / Net I/σ(I): 9.37
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1455 / CC1/2: 0.804 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2420: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BRK

5brk


Resolution: 3.15→44.595 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.74
RfactorNum. reflection% reflection
Rfree0.2982 1000 5.03 %
Rwork0.2333 --
obs0.2367 19880 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15→44.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4715 0 31 0 4746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014871
X-RAY DIFFRACTIONf_angle_d1.2926629
X-RAY DIFFRACTIONf_dihedral_angle_d18.2232851
X-RAY DIFFRACTIONf_chiral_restr0.061728
X-RAY DIFFRACTIONf_plane_restr0.008848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1502-3.31620.42561350.33262707X-RAY DIFFRACTION100
3.3162-3.52390.32231500.27382643X-RAY DIFFRACTION100
3.5239-3.79590.35621330.25532699X-RAY DIFFRACTION100
3.7959-4.17760.29511310.23272694X-RAY DIFFRACTION100
4.1776-4.78150.33461350.21182687X-RAY DIFFRACTION100
4.7815-6.02190.27581600.23932698X-RAY DIFFRACTION100
6.0219-44.59960.24711560.20262752X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.7981 Å / Origin y: -13.6636 Å / Origin z: 19.783 Å
111213212223313233
T0.5771 Å20.0641 Å2-0.0951 Å2-0.4364 Å2-0.0049 Å2--0.6904 Å2
L3.0984 °21.2111 °20.084 °2-1.364 °2-0.0843 °2--1.7696 °2
S0.0937 Å °-0.9606 Å °0.278 Å °0.3043 Å °-0.2705 Å °-0.1846 Å °-0.0896 Å °0.3524 Å °0.0467 Å °
Refinement TLS groupSelection details: all

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