PDB-3v7d: Crystal Structure of ScSkp1-ScCdc4-pSic1 peptide complex

ID or keywords:

Entry

Database: PDB / ID: 3v7d

Title

Crystal Structure of ScSkp1-ScCdc4-pSic1 peptide complex

Components

Cell division control protein 4
Protein SIC1
Suppressor of kinetochore protein 1

Keywords

CELL CYCLE / WD 40 domain / phospho-peptide complex /

E3 ubiquitin ligase /

ligase / phospho binding protein / Sic1 /

phosphorylation

Function / homology

Function and homology information

nuclear SCF ubiquitin ligase complex / RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis /

septin ring assembly ...nuclear SCF ubiquitin ligase complex / RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis /

septin ring assembly / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of exit from mitosis / Antigen processing: Ubiquitination & Proteasome degradation / vacuolar acidification /

kinetochore assembly /

regulation of metabolic process / exit from mitosis / cyclin-dependent protein serine/threonine kinase inhibitor activity / positive regulation of glucose transmembrane transport / protein neddylation / mitotic intra-S DNA damage checkpoint signaling / U3 snoRNA binding / silent mating-type cassette heterochromatin formation /

mitochondrial fusion / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process /

SCF ubiquitin ligase complex / negative regulation of macroautophagy / sporulation resulting in formation of a cellular spore / molecular function inhibitor activity /

DNA replication origin binding / 90S preribosome / regulation of mitotic cell cycle / cullin family protein binding / subtelomeric heterochromatin formation / regulation of protein-containing complex assembly / phosphoserine residue binding /

endomembrane system / negative regulation of cytoplasmic translation / meiotic cell cycle /

ubiquitin binding / G1/S transition of mitotic cell cycle /

kinetochore /

nuclear matrix / G2/M transition of mitotic cell cycle / mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein-containing complex assembly /

chromosome, telomeric region / protein ubiquitination /

cell division /

nucleolus /

nucleus /

cytoplasm
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.306 Å

Authors

Tang, X. / Orlicky, S. / Mittag, T. / Csizmok, V. / Pawson, T. / Forman-Kay, J. / Sicheri, F. / Tyers, M.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Composite low affinity interactions dictate recognition of the cyclin-dependent kinase inhibitor Sic1 by the SCFCdc4 ubiquitin ligase.
Authors: Tang, X. / Orlicky, S. / Mittag, T. / Csizmok, V. / Pawson, T. / Forman-Kay, J.D. / Sicheri, F. / Tyers, M.

History

Deposition	Dec 20, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 2, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2	Sep 13, 2023	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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3v7d.cif.gz	493.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3v7d.ent.gz	406.9 KB	Display	PDB format
PDBx/mmJSON format	3v7d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v7/3v7d ftp://data.pdbj.org/pub/pdb/validation_reports/v7/3v7d	HTTPS FTP

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Related structure data

Related structure data	1nexS 3mks S: Starting model for refinement
Similar structure data	3mks-2 1nex-1 1nex-2 1ev9-d 2vn9-d 2q0g-d 2q0f-d 3d0e-d 3e87-d 5kal-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#60 - Dec 2004 Ubiquitin similarity (16) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (12) #218 - Feb 2018 EPSP Synthase and Weedkillers similarity (12) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (5) #166 - Oct 2013 Proteasome similarity (2) #161 - May 2013 Ricin similarity (2) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1)

Deposited unit

A: Suppressor of kinetochore protein 1

B: Cell division control protein 4

C: Suppressor of kinetochore protein 1

D: Cell division control protein 4

E: Protein SIC1

147 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Suppressor of kinetochore protein 1

B: Cell division control protein 4

E: Protein SIC1

defined by author&software
74.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Suppressor of kinetochore protein 1

D: Cell division control protein 4

defined by author&software
72.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	107.292, 107.292, 166.679
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Suppressor of kinetochore protein 1 / Centromere DNA-binding protein complex CBF3 subunit D / E3 ubiquitin ligase complex SCF subunit SKP1 Mass: 19504.561 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CBF3D, D9798.14, SKP1, YDR328C / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P52286
#2: Protein	Cell division control protein 4 / E3 ubiquitin ligase complex SCF subunit CDC4 / F-box protein CDC4 Mass: 52862.098 Da / Num. of mol.: 2 / Fragment: UNP residues 263-744 / Mutation: C608L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CDC4, YFL009W / Plasmid: pPRO Ex / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07834
#3: Protein/peptide	Protein SIC1 / CDK inhibitor p40 Mass: 2321.288 Da / Num. of mol.: 1 / Fragment: UNP residues 67-85 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38634
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 320 / 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: 3.77 Å³/Da / Density % sol: 67.34 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.5 M Ammonium Sulphate, 0.1 M Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2006 / Details: bent conical Si mirror (Rh coating)
Radiation	Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.31→50 Å / Num. all: 94783 / Num. obs: 94404 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.6 / Redundancy: 5.5 % / R_merge(I) obs: 0.08 / R_sym value: 0.059 / Net I/σ(I): 19.7

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Processing

Software

Name	Version	Classification
PHENIX	1.7.3_928	refinement
MOLREP		phasing
REFMAC	5.6.0117	refinement
HKL-2000		data reduction
HKL-2000		data scaling
ADSC	Quantum	data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1NEX

1nex

Resolution: 2.306→38.021 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.929 / SU ML: 0.36 / Isotropic thermal model: isotropic / σ(F): 1.96 / Phase error: 23.53 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2214	4729	5.02 %
R_work	0.1956	-	-
obs	0.1969	94273	99.61 %
all	-	94783	-

Solvent computation

Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46.094 Å² / k_sol: 0.351 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.1199 Å²	-0 Å²	0 Å²
2-	-	-1.1199 Å²	-0 Å²
3-	-	-	2.2398 Å²

Refinement step

Cycle: LAST / Resolution: 2.306→38.021 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9574	0	0	320	9894

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	9795
X-RAY DIFFRACTION	f_angle_d	0.837	13260
X-RAY DIFFRACTION	f_dihedral_angle_d	12.97	3599
X-RAY DIFFRACTION	f_chiral_restr	0.061	1484
X-RAY DIFFRACTION	f_plane_restr	0.003	1678

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 (%)
2.3057-2.3319	0.3125	127	0.2812	2837	X-RAY DIFFRACTION	92
2.3319-2.3593	0.3411	128	0.2651	2915	X-RAY DIFFRACTION	100
2.3593-2.3881	0.3202	171	0.276	3073	X-RAY DIFFRACTION	100
2.3881-2.4183	0.3302	169	0.2815	2962	X-RAY DIFFRACTION	100
2.4183-2.4501	0.2951	155	0.2794	2991	X-RAY DIFFRACTION	100
2.4501-2.4837	0.3115	156	0.2705	2980	X-RAY DIFFRACTION	100
2.4837-2.5192	0.3045	165	0.2477	3017	X-RAY DIFFRACTION	100
2.5192-2.5568	0.2618	150	0.2387	2979	X-RAY DIFFRACTION	100
2.5568-2.5967	0.2932	166	0.2492	2962	X-RAY DIFFRACTION	100
2.5967-2.6393	0.313	151	0.2316	2985	X-RAY DIFFRACTION	100
2.6393-2.6848	0.2861	187	0.2324	3051	X-RAY DIFFRACTION	100
2.6848-2.7336	0.2371	157	0.2311	2926	X-RAY DIFFRACTION	100
2.7336-2.7861	0.295	172	0.2324	2983	X-RAY DIFFRACTION	100
2.7861-2.843	0.2372	151	0.2288	2986	X-RAY DIFFRACTION	100
2.843-2.9048	0.246	170	0.2237	3008	X-RAY DIFFRACTION	100
2.9048-2.9723	0.2554	170	0.2292	3004	X-RAY DIFFRACTION	100
2.9723-3.0466	0.238	164	0.2228	2995	X-RAY DIFFRACTION	100
3.0466-3.129	0.2928	154	0.2148	2960	X-RAY DIFFRACTION	100
3.129-3.221	0.2244	152	0.2154	2993	X-RAY DIFFRACTION	100
3.221-3.3249	0.2495	154	0.2075	3014	X-RAY DIFFRACTION	100
3.3249-3.4436	0.2347	152	0.2025	2989	X-RAY DIFFRACTION	100
3.4436-3.5814	0.2225	162	0.2	3006	X-RAY DIFFRACTION	100
3.5814-3.7443	0.2133	156	0.1889	2966	X-RAY DIFFRACTION	100
3.7443-3.9415	0.1746	158	0.1715	3028	X-RAY DIFFRACTION	100
3.9415-4.1882	0.2026	154	0.1626	2966	X-RAY DIFFRACTION	100
4.1882-4.5111	0.1611	153	0.138	3026	X-RAY DIFFRACTION	100
4.5111-4.9641	0.1421	139	0.1379	3013	X-RAY DIFFRACTION	100
4.9641-5.6804	0.1936	162	0.1728	3001	X-RAY DIFFRACTION	100
5.6804-7.1489	0.2299	183	0.2054	2973	X-RAY DIFFRACTION	100
7.1489-38.0266	0.1571	141	0.1673	2955	X-RAY DIFFRACTION	99

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	6.8848	1.6867	5.203	6.7282	3.7183	6.1984	0.0126	0.1739	-0.0038	-0.4618	0.4924	-0.1103	-0.6177	-0.3273	-0.4344	0.2703	0.0622	0.1262	0.5068	0.089	0.3366	-46.0681	73.1872	-14.5985
2	8.2144	-0.5489	1.5006	8.3083	-5.0311	4.7224	0.1434	0.7653	-0.125	-0.8851	0.0554	-0.2084	0.8381	-0.3757	-0.0685	0.3772	0.0852	0.0073	0.5417	-0.0112	0.2835	-41.5932	70.3791	-20.4408
3	7.9238	-2.9279	-0.1983	8.1075	-3.0137	1.7238	0.1948	0.2278	-0.6104	-0.2927	-0.0608	0.1787	0.7422	-0.0376	-0.2453	0.3251	0.0287	0.0208	0.3743	0.0541	0.2394	-42.68	64.5034	-13.1852
4	3.5572	1.8714	0.4787	0.9869	0.303	1.4618	-0.0419	0.7573	-0.0964	-0.4462	0.0167	-0.5316	0.5518	0.6565	-0.1659	0.4122	0.2118	0.1601	0.6004	0.1019	0.3802	-29.4823	72.9178	-18.5965
5	3.9304	-0.5898	-2.2669	7.1948	3.3646	2.9561	-0.2334	0.0426	0.6232	-0.4723	-0.0699	-0.93	-0.4218	1.4568	0.2164	0.3199	0.0456	0.0742	0.5329	0.1388	0.57	-24.5073	80.172	-13.6184
6	7.5151	2.8414	2.9132	2.8125	0.4874	3.1048	0.0948	0.3059	-0.0849	-0.0435	-0.1942	-0.475	0.0897	0.0425	0.1282	0.2781	0.117	0.0674	0.3721	0.1066	0.347	-26.7551	70.9299	-7.7171
7	9.3053	-0.0686	-4.9911	6.542	2.1307	9.928	0.0729	0.0256	0.9631	-0.626	-0.2016	-0.5871	-1.5523	0.9772	-0.1275	0.4389	-0.1005	-0.0124	0.4668	0.2331	0.5777	-12.3377	78.0792	2.7017
8	8.3149	-4.371	8.1871	2.4186	-4.4954	8.4322	0.3482	0.0194	0.2088	-0.0522	-0.2115	0.1683	0.0375	0.5082	-0.0803	0.4376	0.0441	-0.0086	0.4993	0.162	0.5141	-15.0759	73.6332	13.2748
9	8.6807	-4.7764	-3.6097	3.9698	1.751	3.2417	-0.0771	1.2845	0.4451	-0.4661	-0.2461	-0.3602	-0.0217	1.4697	0.128	0.4655	-0.0584	-0.0274	0.7566	0.2309	0.7829	-3.7739	67.2608	13.2104
10	3.0955	-1.8239	-1.0661	1.0838	0.6806	0.5789	-0.0497	0.0227	0.127	0.1068	0.2327	0.2064	0.0398	-0.1799	-0.158	0.2862	0.0169	0.0204	0.3396	0.0667	0.3431	-9.2783	59.7237	-0.5002
11	1.1054	0.0443	0.9275	1.2759	0.3338	1.8757	0.4551	0.0831	-0.4388	0.0856	-0.131	-0.0137	0.7405	0.3743	-0.0896	0.3404	0.1269	-0.1238	-0.1006	-0.0921	0.2616	14.4774	39.2266	-17.23
12	4.11	0.994	-1.2424	5.6731	-1.3881	4.6389	0.0051	0.7312	0.1611	-0.6971	0.379	0.4299	0.1066	-0.5178	-0.4082	0.4063	-0.0523	-0.044	0.3614	0.0495	0.2247	-13.8164	39.5746	11.0727
13	4.5407	0.6435	4.4408	7.5751	-0.1288	4.5909	-0.0261	1.153	0.5941	-0.3493	-0.168	0.6358	-0.1397	-0.0331	-0.0494	0.4189	0.0249	-0.0122	0.5846	0.0893	0.3322	-16.4687	41.1603	15.993
14	1.7277	-0.9561	-0.0919	0.9739	-1.1366	3.1696	0.099	0.3613	-0.3853	-0.9653	-0.1694	-0.0747	1.0064	-0.0868	-0.0175	0.6723	-0.0227	0.0586	0.3289	-0.006	0.2827	-3.3577	30.1814	8.9572
15	2.527	-0.857	0.7635	3.3889	-2.7732	2.2719	-0.0542	0.2829	-0.1686	-0.4242	-0.063	-0.2334	0.111	0.1489	0.0317	0.4332	-0.0612	0.0114	0.3066	-0.0389	0.2466	-1.5874	27.7535	18.0465
16	4.9943	0.2216	-0.8445	3.4172	-0.0627	6.2	0.0107	0.3326	0.0644	-0.1442	-0.1083	-0.4966	0.0255	0.9866	0.0256	0.2717	0.0023	0.0651	0.3174	-0.01	0.3314	7.938	17.2081	33.3628
17	4.5206	-1.2397	-2.771	7.2657	3.0381	3.6902	-0.3046	1.462	-0.9208	-1.4672	0.0342	-0.4241	1.937	0.0059	0.3596	0.8586	0.0298	0.0929	0.5052	-0.0732	0.4655	3.7948	4.7699	40.7073
18	4.58	-1.7351	0.496	6.9148	-0.0298	6.594	-0.2204	0.066	-0.1865	-0.0622	0.1581	-0.1437	-0.0515	-0.0439	0.0381	0.2541	-0.077	0.0513	0.2281	-0.0317	0.2532	-2.2746	16.0906	28.8526
19	0.3128	0.7068	-0.0364	3.5418	1.3341	1.0078	0.0763	-0.2055	0.0282	0.3018	-0.2402	0.1893	0.0322	0.0087	0.186	0.3077	-0.0597	-0.0317	0.3501	0.0136	0.2249	-6.8296	-9.3731	23.5533
20	1.7428	0.1055	1.0835	1.1207	-0.4904	1.4552	0.1605	-0.5911	0.0735	0.3011	-0.1055	0.1922	0.1627	-0.4223	-0.0189	0.2981	-0.0712	0.0817	0.3696	-0.0155	0.2072	-23.5924	-29.0388	17.3131
21	1.2808	0.5757	0.5701	1.0545	-0.0667	1.519	-0.0447	-0.0232	0.0803	0.0242	-0.0403	0.0688	0.0695	0.0312	0.0785	0.1878	-0.0109	0.069	0.2133	-0.0279	0.2003	-13.1748	-17.9953	4.1684
22	4.6326	3.9215	0.4813	3.4777	-0.3449	5.3354	-0.2165	0.7443	0.0058	0.5586	0.5879	-1.1451	0.3826	0.7618	-0.1092	0.7987	0.2576	-0.2458	0.8952	-0.1524	0.7731	26.7561	38.1317	-26.3108

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 3:14)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 15:25)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 26:83)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 84:117)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 118:127)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 128:158)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 159:170)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 171:177)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 178:188)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 269:366)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 367:744)
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 4:32)
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 33:83)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 84:117)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 118:158)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 159:177)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 178:188)
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 270:312)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 313:391)
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 392:510)
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 511:744)
22	X-RAY DIFFRACTION	22	chain 'E' and (resseq 71:80)

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