PDB-4bl0: Crystal structure of yeast Bub3-Bub1 bound to phospho-Spc105

ID or keywords:

Entry

Database: PDB / ID: 4bl0

Title

Crystal structure of yeast Bub3-Bub1 bound to phospho-Spc105

Components

CELL CYCLE ARREST PROTEIN BUB3
CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1
SPINDLE POLE BODY COMPONENT SPC105

Keywords

CELL CYCLE / BUBR1 / MAD3 / RAE1 / GLE2 / GLEBS / MAD1 / MAD2 / SPINDLE ASSEMBLY CHECKPOINT / KNL1 / CASC5 / SPC7 / BLINKIN / KINETOCHORE / MITOSIS / CELL DIVISION / ANEUPLOIDY

Function / homology

Function and homology information

bub1-bub3 complex / Inactivation of APC/C via direct inhibition of the APC/C complex / Knl1/Spc105 complex / positive regulation of meiosis I spindle assembly checkpoint / homologous chromosome orientation in meiotic metaphase I / mitotic DNA integrity checkpoint signaling / : / mitotic checkpoint complex / mitotic sister chromatid biorientation / sister chromatid biorientation ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Primorac, I. / Weir, J.R. / Musacchio, A.

Citation

Journal: Elife / Year: 2013
Title: Bub3 Reads Phosphorylated Melt Repeats to Promote Spindle Assembly Checkpoint Signaling
Authors: Primorac, I. / Weir, J.R. / Chiroli, E. / Gross, F. / Hoffmann, I. / Van Gerwen, S. / Ciliberto, A. / Musacchio, A.

History

Deposition	Apr 30, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 18, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2013	Group: Database references
Revision 1.2	Oct 9, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4bl0.cif.gz	324.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4bl0.ent.gz	264.9 KB	Display	PDB format
PDBx/mmJSON format	4bl0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4bl0_validation.pdf.gz	472 KB	Display	wwPDB validaton report
Full document	4bl0_full_validation.pdf.gz	478.2 KB	Display
Data in XML	4bl0_validation.xml.gz	37.9 KB	Display
Data in CIF	4bl0_validation.cif.gz	50.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bl/4bl0 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/4bl0	HTTPS FTP

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Related structure data

Related structure data	213sS S: Starting model for refinement
Similar structure data	6k3d-d 1ku0-2 4dm2-3 6qgp-1 4hzv-d 6qgu-2 3fjn-2 2cy7-d 4hzx-d 2yxv-2 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

Deposited unit

A: CELL CYCLE ARREST PROTEIN BUB3

B: CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1

C: SPINDLE POLE BODY COMPONENT SPC105

D: CELL CYCLE ARREST PROTEIN BUB3

E: CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1

F: SPINDLE POLE BODY COMPONENT SPC105

hetero molecules

99.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: CELL CYCLE ARREST PROTEIN BUB3

E: CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1

F: SPINDLE POLE BODY COMPONENT SPC105

hetero molecules

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

2

A: CELL CYCLE ARREST PROTEIN BUB3

B: CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1

C: SPINDLE POLE BODY COMPONENT SPC105

hetero molecules

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

Unit cell

Length a, b, c (Å)	138.740, 57.900, 118.670
Angle α, β, γ (deg.)	90.00, 102.53, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	CELL CYCLE ARREST PROTEIN BUB3 Mass: 38483.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P26449
#2: Protein	CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 Mass: 8782.949 Da / Num. of mol.: 2 Fragment: EXTENDED BUB3-BINDING MOTIF (A.K.A GLEBS MOTIF), RESIDUES 289-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS References: UniProt: P41695, non-specific serine/threonine protein kinase
#3: Protein/peptide	SPINDLE POLE BODY COMPONENT SPC105 / 105 KDA SPINDLE POLE COMPONENT PROTEIN Mass: 2349.556 Da / Num. of mol.: 2 / Fragment: MELT172, RESIDUES 165-183 / Source method: obtained synthetically / Details: PHOSPHOTHREONINE 172 / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P53148
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	PHOSPHORYLATED AT POSITION T172

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.66 % / Description: NONE
Crystal grow	pH: 7 Details: 0.2M K/ NA TARTRATE, 0.1M BIS TRIS PROPANE PH 7.5, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.21
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2012 / Details: DYNAMICALLY BENDABLE MIRROR
Radiation	Monochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.21 Å / Relative weight: 1
Reflection	Resolution: 1.95→46.8 Å / Num. obs: 66488 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / R_merge(I) obs: 0.07 / Net I/σ(I): 14.15
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 6.3 % / R_merge(I) obs: 1.05 / Mean I/σ(I) obs: 3 / % possible all: 88.1

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.1_1168)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 213S

213s

Resolution: 1.95→46.882 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 19.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1922	3361	5.1 %
R_work	0.1794	-	-
obs	0.18	66483	98.69 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.95→46.882 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6025	0	2	356	6383

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6165
X-RAY DIFFRACTION	f_angle_d	0.964	8372
X-RAY DIFFRACTION	f_dihedral_angle_d	13.057	2229
X-RAY DIFFRACTION	f_chiral_restr	0.066	973
X-RAY DIFFRACTION	f_plane_restr	0.004	1069

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 (%)
1.95-1.9779	0.2696	89	0.2615	2183	X-RAY DIFFRACTION	82
1.9779-2.0074	0.3198	124	0.2662	2402	X-RAY DIFFRACTION	91
2.0074-2.0388	0.2427	143	0.2617	2654	X-RAY DIFFRACTION	100
2.0388-2.0722	0.2543	138	0.2398	2663	X-RAY DIFFRACTION	100
2.0722-2.1079	0.2778	145	0.227	2586	X-RAY DIFFRACTION	100
2.1079-2.1463	0.2121	158	0.2152	2677	X-RAY DIFFRACTION	100
2.1463-2.1875	0.2429	121	0.2151	2646	X-RAY DIFFRACTION	100
2.1875-2.2322	0.2203	149	0.2021	2654	X-RAY DIFFRACTION	100
2.2322-2.2807	0.2303	134	0.2013	2660	X-RAY DIFFRACTION	100
2.2807-2.3338	0.2003	141	0.194	2632	X-RAY DIFFRACTION	100
2.3338-2.3921	0.2119	138	0.1928	2650	X-RAY DIFFRACTION	100
2.3921-2.4568	0.2202	143	0.1878	2636	X-RAY DIFFRACTION	100
2.4568-2.5291	0.2142	148	0.1953	2687	X-RAY DIFFRACTION	100
2.5291-2.6107	0.242	144	0.1997	2631	X-RAY DIFFRACTION	100
2.6107-2.704	0.2254	170	0.1941	2627	X-RAY DIFFRACTION	100
2.704-2.8123	0.2037	154	0.1966	2652	X-RAY DIFFRACTION	100
2.8123-2.9402	0.1666	148	0.1861	2638	X-RAY DIFFRACTION	100
2.9402-3.0952	0.2163	178	0.1779	2648	X-RAY DIFFRACTION	100
3.0952-3.2891	0.2051	126	0.18	2688	X-RAY DIFFRACTION	100
3.2891-3.543	0.1529	137	0.1638	2660	X-RAY DIFFRACTION	99
3.543-3.8994	0.1432	123	0.1436	2683	X-RAY DIFFRACTION	100
3.8994-4.4632	0.1611	140	0.1442	2696	X-RAY DIFFRACTION	100
4.4632-5.6217	0.1571	144	0.1408	2677	X-RAY DIFFRACTION	99
5.6217-46.8955	0.1663	126	0.1783	2792	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	2.4358	-0.1903	0.1565	2.5755	-0.9837	4.0671	-0.1591	-0.1004	0.4341	0.0008	0.0224	0.0358	-0.3888	-0.0332	0.0922	0.205	-0.0729	-0.0549	0.1656	-0.0256	0.2988	2.4525	13.8972	-32.9733
2	4.247	-0.3599	0.225	4.1467	0.3825	3.7239	-0.2311	-0.5677	0.145	0.1728	0.1355	0.2525	-0.0486	-0.5248	0.1413	0.1837	-0.0478	0.0123	0.3831	-0.0187	0.2504	-11.8855	4.1301	-25.7153
3	4.4872	-1.5087	-0.3311	5.4433	1.319	3.6	-0.1199	0.0739	-0.1905	0.2506	-0.2356	0.5201	0.066	-0.5746	0.262	0.1948	-0.0872	0.0137	0.3241	-0.0385	0.2404	-16.9538	0.2332	-38.0407
4	6.1028	-1.0792	1.5454	5.3438	-1.0488	3.0818	0.0826	0.4732	-0.6729	-0.3576	-0.2483	0.5758	0.6278	-0.5962	0.095	0.2437	-0.1243	-0.0408	0.3466	-0.0638	0.2235	-12.9101	-2.9236	-51.4002
5	2.5363	-0.15	1.1218	1.8245	-0.5774	2.6451	0.0375	0.2923	0.1431	-0.1125	-0.0915	-0.0292	-0.0043	0.0078	0.0642	0.1849	-0.0701	0.0049	0.2168	0.0178	0.1749	-0.0233	4.4996	-50.5778
6	7.5681	0.075	1.0507	6.9613	-0.2879	5.9146	0.2123	0.6554	-0.6784	-0.5095	-0.2541	0.5146	0.5362	0.0558	-0.1153	0.3868	-0.0607	-0.0476	0.2328	-0.1029	0.3806	1.0205	-15.5682	-49.1936
7	8.1083	-0.0838	0.4865	4.2345	0.2795	6.7893	0.1052	-0.2646	-0.3804	0.2277	-0.1976	0.7639	0.6845	-0.3755	-0.0398	0.2872	-0.1171	0.0106	0.2036	0.0101	0.3128	-0.2519	-10.1778	-34.8916
8	8.4435	-3.4134	3.4585	8.0164	2.7382	7.894	0.4195	-0.7223	-0.17	0.9547	-0.1202	0.0599	0.555	-0.4052	-0.3513	0.4	-0.1608	-0.0073	0.3155	-0.0307	0.2647	7.3735	-6.6124	-30.3456
9	9.7428	5.7177	-6.7827	4.2289	-5.2632	6.6092	-0.1382	1.1913	0.0508	-0.5478	0.3243	-0.2833	0.9438	-1.3876	-0.412	0.4475	-0.0304	-0.0051	0.6043	-0.005	0.3237	-10.8976	-0.5798	-63.9728
10	6.4608	2.9493	-2.71	4.6797	-5.8583	7.545	0.0802	0.1195	-1.1201	-0.2263	0.2416	0.0969	0.9439	-0.7316	0.0225	0.4671	-0.0794	-0.0888	0.3499	-0.0527	0.5894	-15.9694	-10.9227	-52.2716
11	2.6277	0.6386	-0.0801	4.0176	-0.3931	2.7544	-0.0593	0.2882	0.0183	-0.2045	0.0314	-0.0364	0.0502	0.275	0.013	0.1844	-0.0442	0.0027	0.2242	0.0112	0.1461	29.1893	0.7062	-35.2501
12	3.069	-0.3366	0.7656	2.4884	1.1162	4.439	-0.0484	0.045	-0.4026	0.1989	0.1009	0.0311	0.6679	0.3844	-0.0474	0.3058	0.0485	0.0078	0.1723	0.0108	0.2241	35.6141	-11.9183	-21.227
13	3.4291	-0.4045	0.022	4.0964	0.3241	3.1487	-0.0873	-0.1063	-0.2735	0.246	0.1196	-0.2185	0.3911	0.459	-0.0812	0.2013	0.0373	0.0024	0.2431	0.0146	0.1586	39.9365	-2.2114	-11.7844
14	2.6558	-1.2759	-0.6467	2.2809	0.9791	3.4565	0.0034	-0.129	0.1867	-0.0034	0.0568	-0.1699	-0.2938	0.3499	-0.059	0.1766	-0.1138	0.0037	0.1854	0.0091	0.2066	35.802	12.3735	-10.7456
15	2.0667	0.5375	0.134	1.2368	-0.2277	2.8916	-0.0977	0.0087	0.1756	-0.0324	-0.0109	-0.0983	-0.2811	0.2574	0.1102	0.2264	-0.094	-0.0097	0.1678	0.0005	0.2295	32.225	13.2001	-21.3052
16	4.6218	4.4508	4.2122	4.5455	3.7004	4.3566	-0.0355	-0.6392	0.1716	0.3593	-0.132	-0.0991	-0.0978	0.0321	0.0706	0.3274	-0.0108	0.0251	0.383	-0.0557	0.2331	24.9931	11.8957	0.1426
17	5.8876	1.2802	0.0138	6.0605	1.7807	3.5779	0.0621	-0.5043	-0.2639	0.9708	0.0106	0.4841	0.5827	-0.2035	-0.0237	0.2892	-0.0791	0.0378	0.2828	0.0465	0.153	19.9937	1.0199	-6.9502
18	5.7893	-1.3786	4.8167	7.294	-0.8725	4.0509	0.3259	-0.0565	-0.5096	-0.2944	-0.0686	-0.0488	0.6182	-0.0372	-0.3072	0.2432	-0.079	0.0076	0.2484	-0.0078	0.171	17.5152	-1.0616	-19.0608
19	5.6802	5.2534	-5.226	8.2502	-5.7944	5.0853	-0.0285	0.2194	0.9722	-0.0617	0.6079	-0.1931	-0.9671	0.34	-0.5786	0.4728	-0.2417	-0.0705	0.524	-0.0063	0.4452	44.4831	16.9692	-7.4397
20	3.7108	3.0358	-4.9239	2.8285	-3.2912	8.1239	-0.278	-0.2468	-0.8327	0.7569	0.4142	-0.4942	0.4764	0.2488	0.1673	0.3347	-0.0039	-0.0083	0.2645	0.0164	0.2624	39.0484	3.5608	0.3186

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:106)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 107:154)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 155:206)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 207:244)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 245:340)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 302:327)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 328:341)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 342:347)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 165:171)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 172:176)
11	X-RAY DIFFRACTION	11	(CHAIN D AND RESID 1:106)
12	X-RAY DIFFRACTION	12	(CHAIN D AND RESID 107:178)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 179:234)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 235:263)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 264:340)
16	X-RAY DIFFRACTION	16	(CHAIN E AND RESID 303:317)
17	X-RAY DIFFRACTION	17	(CHAIN E AND RESID 318:334)
18	X-RAY DIFFRACTION	18	(CHAIN E AND RESID 335:347)
19	X-RAY DIFFRACTION	19	(CHAIN F AND RESID 166:171)
20	X-RAY DIFFRACTION	20	(CHAIN F AND RESID 172:177)

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