PDB-5me9: Crystal structure of yeast Cdt1 (N terminal and middle domain), f...

ID or keywords:

Entry

Database: PDB / ID: 5me9

Title

Crystal structure of yeast Cdt1 (N terminal and middle domain), form 1.

Components

Cell division cycle protein CDT1

Keywords

CELL CYCLE / Cdt1 / MCM / winged helix / yeast / DNA replication

Function / homology

Function and homology information

pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear pre-replicative complex / double-strand break repair via break-induced replication / regulation of DNA-templated DNA replication initiation / DNA replication origin binding / cell division / nucleoplasm / nucleus / cytoplasm
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.7 Å

Authors

Pye, V.E. / Frigola, J. / Diffley, J.F.X. / Cherepanov, P.

Citation

Journal: Nat Commun / Year: 2017
Title: Cdt1 stabilizes an open MCM ring for helicase loading.
Authors: Jordi Frigola / Jun He / Kerstin Kinkelin / Valerie E Pye / Ludovic Renault / Max E Douglas / Dirk Remus / Peter Cherepanov / Alessandro Costa / John F X Diffley /

Abstract: ORC, Cdc6 and Cdt1 act together to load hexameric MCM, the motor of the eukaryotic replicative helicase, into double hexamers at replication origins. Here we show that Cdt1 interacts with MCM ...

History

Deposition	Nov 14, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 17, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 5, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Oct 23, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5me9.cif.gz	466 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	5me9.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/me/5me9 ftp://data.pdbj.org/pub/pdb/validation_reports/me/5me9	HTTPS FTP

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Related structure data

Related structure data	3679C 3680C 3681C 5meaC 5mebC 5mecC C: citing same article (ref.)
Similar structure data	5if9-d 4cwd-d 5hk0-d 5mea-d 4q6p-d 2xre-2 4bhg-d 1zag-3 4c5w-d 5c8z-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cell division cycle protein CDT1

B: Cell division cycle protein CDT1

C: Cell division cycle protein CDT1

hetero molecules

151 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cell division cycle protein CDT1

hetero molecules

defined by author
50.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cell division cycle protein CDT1

hetero molecules

defined by author
50.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Cell division cycle protein CDT1

hetero molecules

defined by author
50.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.897, 122.545, 148.393
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Cell division cycle protein CDT1 / SIC1 indispensable protein 2 / Topoisomerase-A hypersensitive protein 11 Mass: 49858.590 Da / Num. of mol.: 3 / Fragment: UNP residues 2-438 Source method: isolated from a genetically manipulated source Details: Residues 1-438 of Cdt1 were recombinantly expressed and purified, residues which are missing in the structure were not defined in the electron density. Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TAH11, CDT1, SID2, YJR046W, J1641 / Production host: Escherichia coli (E. coli) / References: UniProt: P47112
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% Glycerol, 20% PEG 4000, 20% 2-Propanol, 0.1M Tris-HCl pH8.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97934 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 9, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 2.7→74.197 Å / Num. obs: 42303 / % possible obs: 100 % / Redundancy: 11.6 % / R_merge(I) obs: 0.12 / Net I/σ(I): 15.8
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 11.6 % / R_merge(I) obs: 1.4 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
XDS		data reduction
Aimless		data scaling
PHENIX	phenix.autosolve	phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.7→74.197 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.29 / Phase error: 28.99

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2311	4056	5.06 %	Random selection
R_work	0.199	-	-	-
obs	0.2006	42217	99.89 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 81.4 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→74.197 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9047	0	53	92	9192

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	9304
X-RAY DIFFRACTION	f_angle_d	0.767	12659
X-RAY DIFFRACTION	f_dihedral_angle_d	11.865	3440
X-RAY DIFFRACTION	f_chiral_restr	0.031	1501
X-RAY DIFFRACTION	f_plane_restr	0.004	1581

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 (%)
2.7-2.7318	0.3509	184	0.2918	2633	X-RAY DIFFRACTION	100
2.7318-2.7651	0.3631	135	0.2981	2586	X-RAY DIFFRACTION	100
2.7651-2.8001	0.315	140	0.2766	2636	X-RAY DIFFRACTION	100
2.8001-2.8369	0.261	126	0.283	2653	X-RAY DIFFRACTION	100
2.8369-2.8758	0.3269	125	0.2815	2624	X-RAY DIFFRACTION	100
2.8758-2.9169	0.363	140	0.269	2631	X-RAY DIFFRACTION	100
2.9169-2.9604	0.2941	174	0.2698	2640	X-RAY DIFFRACTION	100
2.9604-3.0067	0.362	115	0.2613	2595	X-RAY DIFFRACTION	100
3.0067-3.056	0.2552	137	0.2667	2619	X-RAY DIFFRACTION	100
3.056-3.1087	0.3215	133	0.2658	2609	X-RAY DIFFRACTION	100
3.1087-3.1652	0.2955	120	0.2388	2654	X-RAY DIFFRACTION	100
3.1652-3.2261	0.3407	128	0.2446	2682	X-RAY DIFFRACTION	100
3.2261-3.2919	0.274	150	0.2313	2582	X-RAY DIFFRACTION	100
3.2919-3.3635	0.2409	102	0.2221	2658	X-RAY DIFFRACTION	100
3.3635-3.4418	0.2738	153	0.2166	2637	X-RAY DIFFRACTION	100
3.4418-3.5278	0.2721	134	0.2053	2619	X-RAY DIFFRACTION	100
3.5278-3.6232	0.2594	142	0.2061	2640	X-RAY DIFFRACTION	100
3.6232-3.7298	0.1939	125	0.2035	2599	X-RAY DIFFRACTION	100
3.7298-3.8502	0.2281	142	0.1938	2651	X-RAY DIFFRACTION	100
3.8502-3.9878	0.2396	146	0.1897	2600	X-RAY DIFFRACTION	100
3.9878-4.1475	0.2105	136	0.1695	2635	X-RAY DIFFRACTION	100
4.1475-4.3362	0.1899	125	0.1647	2648	X-RAY DIFFRACTION	100
4.3362-4.5648	0.1516	155	0.1542	2614	X-RAY DIFFRACTION	100
4.5648-4.8507	0.1916	145	0.1541	2615	X-RAY DIFFRACTION	100
4.8507-5.2252	0.1675	120	0.1523	2626	X-RAY DIFFRACTION	100
5.2252-5.7508	0.2196	156	0.178	2607	X-RAY DIFFRACTION	100
5.7508-6.5825	0.2271	170	0.2046	2592	X-RAY DIFFRACTION	100
6.5825-8.2915	0.2295	166	0.1966	2617	X-RAY DIFFRACTION	100
8.2915-74.2245	0.1992	132	0.1796	2589	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	1.6495	0.7858	-0.482	1.9685	0.4309	2.2802	0.0068	-0.2316	0.214	0.1227	0.0878	-0.181	-0.4242	0.2501	-0	0.6748	-0.069	-0.0677	0.6396	-0.0199	0.6696	-39.7574	-32.7126	-46.0234
2	1.2528	-0.2974	-0.1012	2.5478	0.4896	2.9035	-0.0223	-0.2942	0.089	0.3887	-0.0179	-0.0503	-0.232	0.1456	0	0.6543	-0.1187	-0.035	0.6568	0.0101	0.6442	-42.9864	-37.1592	-42.4329
3	0.4426	-0.1624	0.3969	-0.5103	0.077	0.637	0.109	-0.1681	-0.1167	-0.1566	-0.2088	0.1758	-0.9408	-0.274	-0.0003	0.8722	0.0743	0.0108	0.6835	-0.0217	0.8126	-69.2774	-50.3014	-38.191
4	1.5666	0.4724	-1.3294	1.2572	-0.4141	2.1602	0.0269	0.4823	0.0036	-0.297	-0.0362	0.2711	-0.7297	-0.4885	-0	0.824	0.118	-0.0663	0.8639	-0.0481	0.8193	-79.7625	-54.9962	-34.847
5	1.6794	-1.4114	-0.4463	3.5416	0.7564	2.0139	-0.2101	-0.2006	-0.0735	0.5658	0.1683	-0.1254	0.6108	0.294	-0	0.5954	0.1064	0.0209	0.6703	0.0265	0.6148	2.2802	-25.3889	-55.5315
6	1.6058	-0.6443	0.1712	1.3276	1.1443	1.1569	-0.0839	0.1881	-0.204	0.0615	-0.0388	0.1889	0.213	0.0751	1.525	0.3892	0.0345	0.0684	0.3988	0.0035	0.4038	-5.9503	-20.5458	-59.0167
7	0.5921	0.1519	0.3089	0.7784	-0.2079	0.8136	-0.1543	0.0361	-0.0352	-0.1479	0.2162	0.5182	0.42	-0.3453	0	0.8698	-0.1182	-0.067	0.829	0.0403	0.9317	-37.8951	-11.5496	-65.5975
8	1.0545	-1.1751	-0.0503	1.3627	-0.2642	0.7363	0.0383	-0.3513	0.164	-0.1267	-0.0287	0.4156	-0.0359	-0.4067	-0	0.7555	-0.1231	-0.0292	0.8395	-0.0063	0.896	-33.9574	-0.9014	-68.6036
9	2.4598	-1.3604	-0.6781	3.7254	1.8514	1.6442	-0.1076	-0.0253	-0.0367	0.2387	0.1014	-0.0842	0.7418	0.4489	0.0002	0.9558	0.2263	-0.02	0.8628	0.0409	0.7119	3.2862	-26.3057	-8.2279
10	1.5593	-1.0323	-0.6842	1.9139	2.0017	2.5201	0.0096	0.3656	-0.3407	0.0596	-0.4473	0.2539	0.367	-0.0558	-0.0002	0.9734	0.2166	0.0024	0.849	-0.0484	0.7828	-5.6761	-22.2648	-10.3743
11	0.868	-0.182	-0.9716	0.9745	0.3364	1.0991	-0.1713	-0.371	0.0883	0.3483	-0.1264	-0.0212	0.8302	-0.5024	-0.0003	0.9995	-0.1116	-0.0939	0.7567	-0.0261	0.7144	-38.7275	-14.3412	-17.8263
12	1.5756	-0.5111	0.6402	1.3133	-0.3473	1.5014	0.063	-0.2279	-0.0078	0.0483	-0.1286	0.2002	0.5939	-0.1631	-0.0001	0.9113	-0.0425	-0.0552	0.7933	-0.0731	0.8176	-38.3076	-4.9352	-16.6722

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 12:100)
2	X-RAY DIFFRACTION	2	(chain A and resid 101:293)
3	X-RAY DIFFRACTION	3	(chain A and resid 294:334)
4	X-RAY DIFFRACTION	4	(chain A and resid 335:432)
5	X-RAY DIFFRACTION	5	(chain B and resid 12:135)
6	X-RAY DIFFRACTION	6	(chain B and resid 136:301)
7	X-RAY DIFFRACTION	7	(chain B and resid 302:379)
8	X-RAY DIFFRACTION	8	(chain B and resid 380:430)
9	X-RAY DIFFRACTION	9	(chain C and resid 14:137)
10	X-RAY DIFFRACTION	10	(chain C and resid 138:302)
11	X-RAY DIFFRACTION	11	(chain C and resid 303:349)
12	X-RAY DIFFRACTION	12	(chain C and resid 350:431)

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