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- PDB-6g84: Structure of Cdc14 bound to CBK1 PxL motif -

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Basic information

Entry
Database: PDB / ID: 6g84
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 / new mitotic spindle pole body / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring assembly / budding cell apical bud growth / meiotic spindle disassembly / regulation of fungal-type cell wall organization / meiotic nuclear division / cellular bud / prospore membrane ...RENT complex / new mitotic spindle pole body / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring assembly / budding cell apical bud growth / meiotic spindle disassembly / regulation of fungal-type cell wall organization / meiotic nuclear division / cellular bud / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / mitotic spindle pole body / rDNA chromatin condensation / incipient cellular bud site / septum digestion after cytokinesis / cellular bud tip / positive regulation of autophagosome assembly / regulation of exit from mitosis / cellular bud neck / autophagy of mitochondrion / rDNA heterochromatin formation / mating projection tip / serine/threonine protein kinase complex / spindle pole body / cellular response to osmotic stress / negative regulation of transcription by RNA polymerase I / protein serine/threonine phosphatase activity / regulation of protein secretion / establishment or maintenance of cell polarity / MAPK6/MAPK4 signaling / positive regulation of cytokinesis / phosphoprotein phosphatase activity / positive regulation of autophagy / protein tyrosine phosphatase activity / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / protein-tyrosine-phosphatase / non-membrane spanning protein tyrosine phosphatase activity / chromosome segregation / microtubule cytoskeleton organization / cytoplasmic stress granule / spindle pole / mitotic spindle / mitotic cell cycle / 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 / 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 profile. / Dual specificity protein phosphatase domain ...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 profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase CBK1 / Tyrosine-protein phosphatase CDC14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 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 10, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,7068
Polymers89,4994
Non-polymers2084
Water1,74797
1
A: Tyrosine-protein phosphatase CDC14
D: CBK1
B: Tyrosine-protein phosphatase CDC14
C: CBK1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)179,41316
Polymers178,9978
Non-polymers4158
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14110 Å2
ΔGint-93 kcal/mol
Surface area59200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.500, 73.930, 83.530
Angle α, β, γ (deg.)90.00, 114.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-401-

CA

21B-401-

CA

31A-525-

HOH

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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 (strain ATCC 204508 / 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 DC

#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 , 4 types, 101 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 11% PEG3350, 0.2M Calcium Acetate

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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 S 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: 2.47→55.29 Å / Num. obs: 34914 / % possible obs: 99.72 % / Redundancy: 6.5 % / Biso Wilson estimate: 52 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.05 / Net I/av σ(I): 8.16 / Net I/σ(I): 8.16
Reflection shellResolution: 2.47→2.55 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.473 / Num. unique obs: 3456 / CC1/2: 0.666 / Rpim(I) all: 0.63 / Rrim(I) all: 1.6 / % possible all: 99.68

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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: 2.47→55.29 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.42
RfactorNum. reflection% reflection
Rfree0.27 1721 4.93 %
Rwork0.2262 --
obs0.2283 34882 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.47→55.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 7 97 5986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026097
X-RAY DIFFRACTIONf_angle_d0.4158314
X-RAY DIFFRACTIONf_dihedral_angle_d13.1873528
X-RAY DIFFRACTIONf_chiral_restr0.039896
X-RAY DIFFRACTIONf_plane_restr0.0031086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.54270.35041380.3242731X-RAY DIFFRACTION100
2.5427-2.62480.39561530.30932750X-RAY DIFFRACTION100
2.6248-2.71860.30441570.28662732X-RAY DIFFRACTION100
2.7186-2.82750.30371540.2852710X-RAY DIFFRACTION100
2.8275-2.95610.32911420.27412767X-RAY DIFFRACTION100
2.9561-3.1120.37581370.25912739X-RAY DIFFRACTION100
3.112-3.3070.27041520.24672741X-RAY DIFFRACTION100
3.307-3.56230.28321550.24272762X-RAY DIFFRACTION100
3.5623-3.92070.23591380.20832762X-RAY DIFFRACTION100
3.9207-4.4880.22021340.18752791X-RAY DIFFRACTION100
4.488-5.65390.22911240.1922808X-RAY DIFFRACTION100
5.6539-67.06820.26981370.21542868X-RAY DIFFRACTION100
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)
10.0309-0.01340.00080.02090.04740.15440.34530.0346-0.41070.0231-0.22920.50310.1735-0.32590.00320.5662-0.06810.03250.5766-0.03590.74492.183-53.16517.8276
20.4623-0.21960.19930.1042-0.09390.0847-0.0861-0.59140.09830.1580.039-0.1039-0.0168-0.29760.01040.5762-0.12090.03710.6386-0.01510.408510.2426-38.636517.6924
30.3960.1275-0.1050.2304-0.03190.47080.1492-0.3084-0.0306-0.0578-0.23820.0678-0.0381-0.0595-0.00030.5062-0.0924-0.04060.53220.06840.472413.6757-45.158111.3003
40.0311-0.0195-0.0220.06930.06190.0558-0.0562-0.0702-0.2620.1087-0.1558-0.08240.04050.022-0.00020.47240.0084-0.05590.37940.12250.54627.8705-45.954512.8554
50.1388-0.0934-0.0510.3302-0.09560.08260.3316-0.80840.18810.23-0.3428-0.20040.0612-0.10910.09070.7142-0.2504-0.02760.88690.00370.564731.6169-31.176931.3059
60.43140.42720.32970.48260.2470.33490.2018-0.13840.088-0.0251-0.0633-0.09450.02130.07930.0020.4439-0.0401-0.01090.56750.01950.513140.3684-29.335315.2569
70.00580.00790.00110.0113-0.00470.0377-0.00230.0156-0.01740.1321-0.04030.0140.0597-0.047901-0.0406-0.04440.91890.27061.066618.49-60.21779.7244
80.0177-0.0066-0.00790.0214-0.03160.06410.293-0.00740.12410.36330.01960.2368-0.2897-0.0906-0.00070.50730.06080.08950.4874-0.05010.76155.0742-16.4421-5.092
90.8137-0.4524-0.28790.80580.53130.5470.14530.31320.1342-0.136-0.173-0.08280.00270.00730.00010.48440.06090.02910.52020.14740.495427.6866-34.695-18.2228
100.0029-0.00270.00170.0035-0.00520.0124-0.08870.0929-0.0645-0.1429-0.10070.0557-0.0066-0.0438-0.00010.77280.0186-0.19130.81440.13390.932219.2474-10.6954-14.4319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 140 )
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 163 )
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 236 )
6X-RAY DIFFRACTION6chain 'A' and (resid 237 through 371 )
7X-RAY DIFFRACTION7chain 'D' and (resid 85 through 91 )
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 22 )
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 371 )
10X-RAY DIFFRACTION10chain 'C' and (resid 81 through 91 )

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