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- PDB-9s1s: Crystal structure of C278S mutant of mouse CDC14A in complex with... -

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Basic information

Entry
Database: PDB / ID: 9s1s
TitleCrystal structure of C278S mutant of mouse CDC14A in complex with a model phosphopeptide
Components
  • Dual specificity protein phosphatase CDC14A
  • Model phosphohexapeptide
KeywordsCELL CYCLE / CDC14A / DUAL SPECIFICITY PHOSPHATASE / HEARING LOSS / STRUCTURAL-FUNCTIONAL RELATIONSHIP
Function / homology
Function and homology information


kinociliary basal body / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / stereocilium tip / kinocilium / MAPK6/MAPK4 signaling / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / sensory perception of sound ...kinociliary basal body / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / stereocilium tip / kinocilium / MAPK6/MAPK4 signaling / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / sensory perception of sound / spindle pole / cell division / centrosome / endoplasmic reticulum / nucleoplasm / cytosol
Similarity search - Function
Dual specificity/tyrosine protein phosphatase, N-terminal / Dual-specificity phosphatase CDC14, C-terminal / Dual specificity protein phosphatase, N-terminal half / : / Polymorphic toxin system, DSP-PTPase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...Dual specificity/tyrosine protein phosphatase, N-terminal / Dual-specificity phosphatase CDC14, C-terminal / Dual specificity protein phosphatase, N-terminal half / : / Polymorphic toxin system, DSP-PTPase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Dual specificity protein phosphatase CDC14A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.62 Å
AuthorsShabbir, K. / Jackisch, G. / Sele, C. / Murina, V. / Knecht, W. / Wilson, E. / Dong, L. / Friedman, T.B. / Imtiaz, A. / Logan, D.T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2023-05074 Sweden
CitationJournal: To Be Published
Title: CDC14A truncated mouse model mimics human deafness variants, with functional evidence of phosphatase activity
Authors: Shabbir, K. / Jackisch, G. / Knecht, W. / Sele, C. / Murina, V. / Wilson, E. / Dong, L. / Friedman, T.B. / Imtiaz, A. / Logan, D.T.
History
DepositionJul 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase CDC14A
B: Dual specificity protein phosphatase CDC14A
E: Model phosphohexapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,16411
Polymers80,4163
Non-polymers7498
Water11,115617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-75 kcal/mol
Surface area31220 Å2
Unit cell
Length a, b, c (Å)102.342, 158.093, 69.274
Angle α, β, γ (deg.)90.000, 124.593, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Dual specificity protein phosphatase CDC14A / CDC14 cell division cycle 14 homolog A


Mass: 39795.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdc14a / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: Q6GQT0, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Protein/peptide Model phosphohexapeptide


Mass: 824.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium sulphate; polymer: 20% (w/v) polyethylene glycol 3350; Buffer: 0.1M Bis-Tris propane, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.72931 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72931 Å / Relative weight: 1
ReflectionResolution: 1.62→79.05 Å / Num. obs: 79380 / % possible obs: 69.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 18.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.047 / Rrim(I) all: 0.127 / Net I/σ(I): 9.9
Reflection shellResolution: 1.72→1.78 Å / Rmerge(I) obs: 1.585 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3969 / CC1/2: 0.452 / Rpim(I) all: 0.628 / Rrim(I) all: 0.127

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIX1.21rc1_5127phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.62→28.82 Å / SU ML: 0.1746 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6276
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2067 3978 5.01 %
Rwork0.1678 75364 -
obs0.1698 79342 69.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.42 Å2
Refinement stepCycle: LAST / Resolution: 1.62→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5582 0 45 617 6244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00895845
X-RAY DIFFRACTIONf_angle_d0.90637897
X-RAY DIFFRACTIONf_chiral_restr0.0504807
X-RAY DIFFRACTIONf_plane_restr0.00921014
X-RAY DIFFRACTIONf_dihedral_angle_d14.29352154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.640.361620.232853X-RAY DIFFRACTION1.35
1.64-1.660.389170.2723200X-RAY DIFFRACTION5.09
1.66-1.680.2901200.2655348X-RAY DIFFRACTION9.04
1.68-1.70.3067290.2743515X-RAY DIFFRACTION13.49
1.7-1.730.3105320.2857684X-RAY DIFFRACTION17.35
1.73-1.750.229540.281969X-RAY DIFFRACTION25.3
1.75-1.780.2979610.27631208X-RAY DIFFRACTION31.03
1.78-1.810.275730.26461468X-RAY DIFFRACTION37.62
1.81-1.840.2971980.26791772X-RAY DIFFRACTION46.14
1.84-1.880.26191200.25592147X-RAY DIFFRACTION55.2
1.88-1.910.28111150.24082528X-RAY DIFFRACTION65.08
1.91-1.950.26841490.22632804X-RAY DIFFRACTION72.41
1.95-1.990.28551610.2283118X-RAY DIFFRACTION79.86
1.99-2.040.28011770.21773395X-RAY DIFFRACTION86.55
2.04-2.090.2631940.20783604X-RAY DIFFRACTION93.41
2.09-2.150.24282000.19493794X-RAY DIFFRACTION97.99
2.15-2.210.2212080.18273868X-RAY DIFFRACTION99.54
2.21-2.280.21642030.1733907X-RAY DIFFRACTION100
2.28-2.360.22132270.16963865X-RAY DIFFRACTION100
2.36-2.460.20282170.16993882X-RAY DIFFRACTION100
2.46-2.570.19472080.16923877X-RAY DIFFRACTION100
2.57-2.710.20611990.16833880X-RAY DIFFRACTION100
2.71-2.870.21442160.17063902X-RAY DIFFRACTION100
2.87-3.10.20161740.16043919X-RAY DIFFRACTION100
3.1-3.410.20012280.15233882X-RAY DIFFRACTION100
3.41-3.90.18082060.13193916X-RAY DIFFRACTION100
3.9-4.910.15511900.11563929X-RAY DIFFRACTION100
4.91-28.820.17142100.16023930X-RAY DIFFRACTION99.57

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