PDB-6g86: Structure of Cdc14 bound to SIC1 PxL motif

ID or keywords:

Entry

Database: PDB / ID: 6g86

Title

Structure of Cdc14 bound to SIC1 PxL motif

Components

Protein SIC1
Tyrosine-protein phosphatase CDC14

Keywords

CELL CYCLE / CDC14 / phosphatase / PXL / SIC1

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 / meiotic spindle disassembly / protein tyrosine/serine/threonine phosphatase activity / positive regulation of autophagosome assembly / autophagy of mitochondrion / regulation of exit from mitosis / rDNA heterochromatin formation / cellular bud neck ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.74 Å

Authors

Mouilleron, S. / Kataria, M. / Uhlmann, F.

Citation

Journal: 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

Deposition	Apr 7, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 17, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2018	Group: 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 1.2	Dec 19, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 17, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6g86.cif.gz	326.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6g86_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	6g86_full_validation.pdf.gz	1.3 MB	Display
Data in XML	6g86_validation.xml.gz	36.9 KB	Display
Data in CIF	6g86_validation.cif.gz	55.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g8/6g86 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/6g86	HTTPS FTP

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Related structure data

Related structure data	6g84C 6g85C 1ohcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2ycw-d 2wqz-1 3n9u-d 1m2o-2 5xw5-d 2qvs-d 3no6-d 1m2o-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (9) #126 - Jun 2010 Epidermal Growth Factor similarity (8) #225 - Sep 2018 Phytase similarity (5) #166 - Oct 2013 Proteasome similarity (1) #161 - May 2013 Ricin similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: Tyrosine-protein phosphatase CDC14

B: Tyrosine-protein phosphatase CDC14

D: Protein SIC1

C: Protein SIC1

hetero molecules

91.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	75.090, 94.321, 127.656
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein / Protein/peptide , 2 types, 4 molecules ABDC

#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 (brewer's yeast) Gene: CDC14, OAF3, YFR028C / Production host: Escherichia coli (E. coli) / References: UniProt: Q00684, protein-tyrosine-phosphatase
#2: Protein/peptide	Protein SIC1 / CDK inhibitor p40 Mass: 1670.945 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38634

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Non-polymers , 5 types, 720 molecules

#3: 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
#4: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH6, 18% PEG200, 5% PEG 3000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.28 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 29, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.28 Å / Relative weight: 1
Reflection	Resolution: 1.74→63.8 Å / Num. obs: 93481 / % possible obs: 99.6 % / Redundancy: 5.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.06 / Net I/σ(I): 11.8
Reflection shell	Resolution: 1.74→1.8 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.95 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 42727 / CC_1/2: 0.52 / R_pim(I) all: 0.5 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1OHC

1ohc

Resolution: 1.74→63.8 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.14

	R_factor	Num. reflection	% reflection
R_free	0.1987	4627	4.97 %
R_work	0.1655	-	-
obs	0.1671	93155	99.57 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.74→63.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5973	0	109	708	6790

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6401
X-RAY DIFFRACTION	f_angle_d	1.017	8699
X-RAY DIFFRACTION	f_dihedral_angle_d	7.091	5757
X-RAY DIFFRACTION	f_chiral_restr	0.067	920
X-RAY DIFFRACTION	f_plane_restr	0.007	1127

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7399-1.7597	0.3786	156	0.3354	2830	X-RAY DIFFRACTION	97
1.7597-1.7804	0.4095	147	0.3184	2896	X-RAY DIFFRACTION	99
1.7804-1.8021	0.3175	139	0.2944	2918	X-RAY DIFFRACTION	99
1.8021-1.8249	0.3212	155	0.2807	2932	X-RAY DIFFRACTION	99
1.8249-1.8489	0.3192	149	0.2725	2890	X-RAY DIFFRACTION	99
1.8489-1.8742	0.2959	120	0.2609	2925	X-RAY DIFFRACTION	99
1.8742-1.901	0.2742	128	0.2438	2927	X-RAY DIFFRACTION	99
1.901-1.9294	0.2567	168	0.2292	2918	X-RAY DIFFRACTION	100
1.9294-1.9595	0.2554	190	0.2212	2865	X-RAY DIFFRACTION	100
1.9595-1.9917	0.2377	157	0.2038	2918	X-RAY DIFFRACTION	99
1.9917-2.026	0.2486	163	0.1952	2926	X-RAY DIFFRACTION	100
2.026-2.0629	0.2455	157	0.1876	2921	X-RAY DIFFRACTION	100
2.0629-2.1025	0.2183	145	0.181	2929	X-RAY DIFFRACTION	100
2.1025-2.1455	0.2126	166	0.1811	2959	X-RAY DIFFRACTION	100
2.1455-2.1921	0.179	132	0.1738	2945	X-RAY DIFFRACTION	100
2.1921-2.2431	0.2106	163	0.1643	2921	X-RAY DIFFRACTION	100
2.2431-2.2992	0.1857	158	0.1591	2948	X-RAY DIFFRACTION	100
2.2992-2.3614	0.2046	165	0.1579	2920	X-RAY DIFFRACTION	100
2.3614-2.4309	0.2061	144	0.1571	2964	X-RAY DIFFRACTION	100
2.4309-2.5093	0.1798	165	0.1513	2962	X-RAY DIFFRACTION	100
2.5093-2.599	0.2023	163	0.1486	2935	X-RAY DIFFRACTION	100
2.599-2.7031	0.1803	165	0.1428	2945	X-RAY DIFFRACTION	100
2.7031-2.8261	0.1941	147	0.1559	2968	X-RAY DIFFRACTION	100
2.8261-2.9751	0.1718	149	0.1553	2976	X-RAY DIFFRACTION	100
2.9751-3.1615	0.2179	156	0.1582	2997	X-RAY DIFFRACTION	100
3.1615-3.4056	0.2089	172	0.1585	2981	X-RAY DIFFRACTION	100
3.4056-3.7482	0.1865	153	0.1504	3011	X-RAY DIFFRACTION	100
3.7482-4.2905	0.1461	142	0.1253	3036	X-RAY DIFFRACTION	100
4.2905-5.4052	0.1452	164	0.1295	3046	X-RAY DIFFRACTION	100
5.4052-63.871	0.1716	149	0.1633	3219	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.4167	-0.0229	0.0013	0.0898	0.0443	0.1893	0.1832	-0.3119	0.2315	0.1001	-0.0149	0.042	-0.1586	0.3876	0.0697	0.2587	-0.097	0.0021	0.2941	-0.1087	0.2268	37.6518	53.569	55.047
2	0.4906	0.3932	-0.2822	0.3018	-0.0694	0.7137	0.0953	-0.0996	0.0597	0.0551	-0.0919	0.0127	-0.039	0.0659	0.0002	0.1585	-0.0098	-0.0148	0.1613	-0.0125	0.151	30.5526	43.9537	45.9431
3	0.864	0.5605	-0.0529	0.625	-0.1566	0.5752	0.0192	0.0031	0.0009	0.045	-0.0413	0.0722	0.0456	0.0014	0	0.1441	0.0025	0.0042	0.1237	-0.01	0.1559	14.3462	25.5324	35.7615
4	0.2419	-0.0986	-0.0253	0.0674	0.0758	0.3233	0	-0.1273	0.0281	0.0215	0.032	-0.2381	0.246	0.2749	0.0193	0.2298	0.1139	-0.054	0.2944	0.003	0.3838	59.6103	34.988	28.1991
5	0.7226	0.1505	0.093	0.4261	-0.0003	1.0548	0.0191	0.0254	-0.0583	-0.0085	-0.0133	-0.0904	0.08	0.094	-0	0.1405	0.0246	-0.0085	0.1499	-0.0084	0.1794	46.8668	41.1954	22.1714
6	0.1543	0.0616	0.0336	0.2045	-0.1441	0.6301	-0.0373	0.1832	0.1784	-0.1838	-0.0214	-0.0923	-0.139	0.1045	0.0002	0.2707	-0.0304	0.0049	0.2352	0.0671	0.2362	39.3585	62.6068	2.8453
7	0.6125	0.1821	-0.1107	-0.0286	0.117	0.7758	-0.0541	0.0789	0.0814	-0.0399	0.0465	-0.047	-0.1012	-0.1351	0.033	0.1502	0.0087	-0.0373	0.1902	0.0366	0.1311	23.4238	53.1846	11.0228
8	0.0065	-0.0233	-0.0173	0.017	0.002	0.0042	-0.0932	-0.1422	0.0525	-0.0827	-0.2377	0.2232	-0.1849	-0.1964	-0	0.5123	0.049	0.1498	0.3137	-0.0284	0.4603	20.261	56.3895	51.2065
9	-0.0098	-0.0022	-0.0096	0.014	0.0069	0.0045	0.0935	0.2864	-0.222	0.0041	-0.1401	0.0223	0.0556	0.1307	0.0001	0.5444	0.1339	0.0822	0.3331	0.0114	0.4603	51.5671	29.251	13.049

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 41 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 42 through 153 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 154 through 370 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 7 through 42 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 43 through 163 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 164 through 235 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 236 through 373 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 52 through 61 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 51 through 61 )

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