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- PDB-6g85: Structure of Cdc14 bound to CBK1 PxL motif -

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Basic information

Entry
Database: PDB / ID: 6g85
TitleStructure of Cdc14 bound to CBK1 PxL motif
Components
  • (CBK1) x 2
  • Tyrosine-protein phosphatase CDC14
KeywordsCELL CYCLE / CDC14 / phosphatase / PXL / CBK1
Function / homology
Function and homology information


RENT complex / positive regulation of mitotic actomyosin contractile ring assembly / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of fungal-type cell wall organization / budding cell apical bud growth / meiotic spindle disassembly / cellular bud / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / incipient cellular bud site ...RENT complex / positive regulation of mitotic actomyosin contractile ring assembly / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of fungal-type cell wall organization / budding cell apical bud growth / meiotic spindle disassembly / cellular bud / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / incipient cellular bud site / cellular bud tip / protein tyrosine/serine/threonine phosphatase activity / septum digestion after cytokinesis / serine/threonine protein kinase complex / positive regulation of autophagosome assembly / autophagy of mitochondrion / regulation of exit from mitosis / rDNA heterochromatin formation / cellular bud neck / mating projection tip / spindle pole body / cellular response to osmotic stress / actomyosin structure organization / establishment or maintenance of cell polarity / protein serine/threonine phosphatase activity / regulation of protein secretion / MAPK6/MAPK4 signaling / positive regulation of cytokinesis / phosphoprotein phosphatase activity / mitotic cytokinesis / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / chromosome segregation / mitotic spindle / spindle pole / cytoplasmic stress granule / microtubule cytoskeleton organization / actin cytoskeleton / mitotic cell cycle / cell cortex / non-specific serine/threonine protein kinase / intracellular signal transduction / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Dual specificity/tyrosine protein phosphatase, N-terminal / Dual-specificity phosphatase CDC14, C-terminal / Dual specificity protein phosphatase, N-terminal half / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal ...Dual specificity/tyrosine protein phosphatase, N-terminal / Dual-specificity phosphatase CDC14, C-terminal / Dual specificity protein phosphatase, N-terminal half / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / 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
DI(HYDROXYETHYL)ETHER / Serine/threonine-protein kinase CBK1 / Tyrosine-protein phosphatase CDC14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.528 Å
AuthorsMouilleron, S. / Kataria, M. / Uhlmann, F.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: A PxL motif promotes timely cell cycle substrate dephosphorylation by the Cdc14 phosphatase.
Authors: Kataria, M. / Mouilleron, S. / Seo, M.H. / Corbi-Verge, C. / Kim, P.M. / Uhlmann, F.
History
DepositionApr 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase CDC14
B: Tyrosine-protein phosphatase CDC14
C: CBK1
D: CBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,40113
Polymers89,4994
Non-polymers9029
Water14,448802
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-11 kcal/mol
Surface area31640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.154, 97.408, 129.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tyrosine-protein phosphatase CDC14


Mass: 42975.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: CDC14, OAF3, YFR028C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): pLysS / References: UniProt: Q00684, protein-tyrosine-phosphatase

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Protein/peptide , 2 types, 2 molecules CD

#2: Protein/peptide CBK1


Mass: 1737.926 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53894*PLUS
#3: Protein/peptide CBK1


Mass: 1809.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53894*PLUS

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Non-polymers , 6 types, 811 molecules

#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 802 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.5% PEG 6000 and 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.52→48.7 Å / Num. obs: 145196 / % possible obs: 97.3 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Net I/σ(I): 10.6
Reflection shellResolution: 1.52→1.58 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 64686 / Rpim(I) all: 0.45 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OHC

1ohc


Resolution: 1.528→59.995 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 7061 4.98 %
Rwork0.182 --
obs0.1834 141666 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.528→59.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5978 0 54 802 6834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.026469
X-RAY DIFFRACTIONf_angle_d1.3078837
X-RAY DIFFRACTIONf_dihedral_angle_d16.1843870
X-RAY DIFFRACTIONf_chiral_restr0.097940
X-RAY DIFFRACTIONf_plane_restr0.0091156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5284-1.54580.39382180.36354032X-RAY DIFFRACTION88
1.5458-1.5640.35232310.36354279X-RAY DIFFRACTION95
1.564-1.5830.38222160.33594403X-RAY DIFFRACTION96
1.583-1.60310.39882250.32754349X-RAY DIFFRACTION96
1.6031-1.62420.31642360.29734460X-RAY DIFFRACTION97
1.6242-1.64640.30632260.28644419X-RAY DIFFRACTION97
1.6464-1.670.31532230.27424459X-RAY DIFFRACTION97
1.67-1.69490.28072200.27344496X-RAY DIFFRACTION98
1.6949-1.72140.31352510.2594432X-RAY DIFFRACTION97
1.7214-1.74960.31731940.25664472X-RAY DIFFRACTION97
1.7496-1.77980.28452470.24134416X-RAY DIFFRACTION97
1.7798-1.81210.28852470.24244459X-RAY DIFFRACTION98
1.8121-1.8470.27782210.23614494X-RAY DIFFRACTION97
1.847-1.88470.24872390.22884434X-RAY DIFFRACTION97
1.8847-1.92570.27642090.23634451X-RAY DIFFRACTION97
1.9257-1.97050.22152530.21384438X-RAY DIFFRACTION97
1.9705-2.01970.22942450.20244477X-RAY DIFFRACTION98
2.0197-2.07440.23952140.18564524X-RAY DIFFRACTION98
2.0744-2.13540.21842430.18564522X-RAY DIFFRACTION98
2.1354-2.20430.19632200.17614543X-RAY DIFFRACTION98
2.2043-2.28310.20162530.17424484X-RAY DIFFRACTION98
2.2831-2.37450.21492600.17244482X-RAY DIFFRACTION98
2.3745-2.48260.19892490.17444498X-RAY DIFFRACTION98
2.4826-2.61350.20892340.16534549X-RAY DIFFRACTION98
2.6135-2.77720.21142650.16794542X-RAY DIFFRACTION99
2.7772-2.99170.21952330.16714600X-RAY DIFFRACTION99
2.9917-3.29270.18642450.15864602X-RAY DIFFRACTION99
3.2927-3.76910.16732570.15894670X-RAY DIFFRACTION99
3.7691-4.74840.14912330.13654719X-RAY DIFFRACTION99
4.7484-60.04150.192540.16944900X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 30.5076 Å / Origin y: 42.8771 Å / Origin z: 28.7415 Å
111213212223313233
T0.1424 Å20.0239 Å2-0.019 Å2-0.1375 Å2-0.0035 Å2--0.1215 Å2
L0.7779 °20.1539 °2-0.1577 °2-0.6173 °2-0.0121 °2--0.7152 °2
S-0.0207 Å °0.0478 Å °0.0365 Å °0.007 Å °0.0076 Å °0.0037 Å °-0.0294 Å °0.0242 Å °0.0136 Å °
Refinement TLS groupSelection details: all

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