PDB-4c9y: Structural Basis for the microtubule binding of the human kinetoc...

ID or keywords:

Entry

Database: PDB / ID: 4c9y

Title

Structural Basis for the microtubule binding of the human kinetochore Ska complex

Components

SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1

Keywords

CELL CYCLE / CELL DIVISON / KINETOCHORE-MICROTUBULE ATTACHMENT / WINGED-HELIX DOMAIN

Function / homology

Function and homology information

outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / intercellular bridge / centriolar satellite / regulation of microtubule polymerization or depolymerization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / chromosome segregation ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.01 Å

Authors

Abad, M. / Medina, B. / Santamaria, A. / Zou, J. / Plasberg-Hill, C. / Madhumalar, A. / Jayachandran, U. / Redli, P.M. / Rappsilber, J. / Nigg, E.A. / Jeyaprakash, A.A.

Citation

Journal: Nat.Commun. / Year: 2014
Title: Structural Basis for Microtubule Recognition by the Human Kinetochore Ska Complex.
Authors: Abad, M.A. / Medina, B. / Santamaria, A. / Zou, J. / Plasberg-Hill, C. / Madhumalar, A. / Jayachandran, U. / Redli, P.M. / Rappsilber, J. / Nigg, E.A. / Jeyaprakash, A.A.

History

Deposition	Oct 4, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 22, 2014	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4c9y.cif.gz	115.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4c9y.ent.gz	97.8 KB	Display	PDB format
PDBx/mmJSON format	4c9y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4c9y_validation.pdf.gz	431 KB	Display	wwPDB validaton report
Full document	4c9y_full_validation.pdf.gz	433.2 KB	Display
Data in XML	4c9y_validation.xml.gz	12.4 KB	Display
Data in CIF	4c9y_validation.cif.gz	17.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/4c9y ftp://data.pdbj.org/pub/pdb/validation_reports/c9/4c9y	HTTPS FTP

-
Related structure data

Related structure data	4ca0C C: citing same article (ref.)
Similar structure data	1fso-d 3uiy-d 2kjw-d 5h4b-d 3uiz-4 3uiz-3 4pug-1 5f1l-1 5v6h-2 6j08-2 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (5) #245 - May 2020 Spliceosomes similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1

B: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1

29.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1

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

2

B: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1

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

Unit cell

Length a, b, c (Å)	39.006, 161.578, 104.482
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-2066- HOH
2	1	B-2004- HOH

#1: Protein	SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1 / SKA1 Mass: 14653.601 Da / Num. of mol.: 2 / Fragment: MT-BINDING DOMAIN, RESDUES 133-255 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC-CDF-HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q96BD8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	SELENOMETHIONINE LABELED

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 57 % / Description: NONE
Crystal grow	pH: 7.5 Details: 0.1M IMIDAZOLE-MES BUFFER, 0.09 M NPS MIX AND 30% EDO_P8K, pH 7.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.28
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.28 Å / Relative weight: 1
Reflection	Resolution: 2→63.9 Å / Num. obs: 22542 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / B_iso Wilson estimate: 32.79 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 15.2
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 3.8 / % possible all: 99.6

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2.01→43.868 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 26.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2462	2347	10.44 %
R_work	0.194	-	-
obs	0.1994	22475	99.64 %

Solvent computation

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

Displacement parameters

B_iso mean: 52.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.01→43.868 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2026	0	0	135	2161

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2062
X-RAY DIFFRACTION	f_angle_d	1.094	2767
X-RAY DIFFRACTION	f_dihedral_angle_d	14.482	797
X-RAY DIFFRACTION	f_chiral_restr	0.078	312
X-RAY DIFFRACTION	f_plane_restr	0.005	345

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 (%)
2.01-2.051	0.2938	135	0.2335	1161	X-RAY DIFFRACTION	99
2.051-2.0956	0.2876	159	0.2377	1118	X-RAY DIFFRACTION	99
2.0956-2.1444	0.2971	128	0.2292	1168	X-RAY DIFFRACTION	99
2.1444-2.198	0.2748	132	0.2178	1169	X-RAY DIFFRACTION	99
2.198-2.2574	0.2794	123	0.2007	1183	X-RAY DIFFRACTION	100
2.2574-2.3239	0.2519	146	0.189	1149	X-RAY DIFFRACTION	99
2.3239-2.3989	0.2367	133	0.2093	1164	X-RAY DIFFRACTION	100
2.3989-2.4846	0.2742	130	0.1963	1186	X-RAY DIFFRACTION	100
2.4846-2.5841	0.284	138	0.1957	1187	X-RAY DIFFRACTION	100
2.5841-2.7016	0.2719	142	0.2002	1158	X-RAY DIFFRACTION	100
2.7016-2.8441	0.2506	136	0.2009	1197	X-RAY DIFFRACTION	100
2.8441-3.0222	0.2923	150	0.2093	1176	X-RAY DIFFRACTION	100
3.0222-3.2555	0.2345	118	0.1989	1214	X-RAY DIFFRACTION	100
3.2555-3.583	0.2322	144	0.1932	1185	X-RAY DIFFRACTION	100
3.583-4.1011	0.2165	129	0.1734	1209	X-RAY DIFFRACTION	100
4.1011-5.1656	0.21	147	0.1672	1219	X-RAY DIFFRACTION	100
5.1656-43.8789	0.2511	157	0.2035	1285	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	4.689	1.9465	-1.889	3.9645	-5.3093	7.2658	-0.2665	0.1101	0.2048	-0.1182	-0.2544	-0.3433	-0.4758	-0.2233	0.4093	0.7212	0.1309	0.106	0.4325	0.0639	0.4815	9.6053	11.2337	21.4242
2	5.7406	-5.2137	-2.0154	5.7699	3.5767	5.5349	0.1756	0.4191	-0.8666	-0.2842	-0.8453	0.8061	0.7277	-0.2029	0.5876	0.8653	0.0351	0.1366	0.4537	-0.0188	0.8022	2.5633	-5.0647	18.4452
3	0.9548	0.3544	0.6114	1.649	-0.7789	2.0389	-0.6439	-0.1479	-0.5367	-0.5299	0.3449	-0.7074	0.8267	0.4803	0.2122	0.4827	0.1184	0.2717	0.2624	0.0793	0.4733	10.8032	12.232	13.829
4	1.442	1.9098	0.6549	7.7345	0.9761	0.4426	0.1627	-0.3865	0.6118	1.2817	0.1179	0.7479	-0.4866	-0.4351	-0.2246	0.6553	0.0032	0.0584	0.4001	-0.0503	0.3837	13.7983	33.6648	10.9149
5	5.6977	4.2197	-5.5494	6.823	-4.6666	5.6789	0.2857	0.7933	0.9434	-0.0847	0.4065	0.5078	-0.4558	-0.5395	-0.6682	0.435	0.0177	0.0519	0.2707	0.0261	0.2778	5.8122	29.4415	6.1051
6	4.7879	-1.916	1.964	8.4516	0.4731	4.6036	-0.0495	0.1782	0.4329	0.0051	0.2901	0.5976	-0.3261	-0.9962	-0.3391	0.5164	0.0466	0.1435	0.3555	0.0932	0.4352	1.5537	20.8606	12.5864
7	7.7184	5.2239	-5.6628	7.2591	-4.8607	5.2034	-0.2853	1.861	0.186	-1.2897	0.45	0.6072	-0.0647	-2.3115	0.0416	0.8185	0.0269	0.1553	0.6462	-0.0728	0.5569	1.7351	5.0411	9.6394
8	2.1377	0.4975	0.2277	6.9757	-4.2703	9.6766	0.1329	1.0906	-0.0223	-0.2899	0.6244	1.3388	0.6764	-1.0789	-0.3112	0.2321	0.0012	0.2199	0.5675	0.1717	0.6657	-2.7087	11.102	18.2824
9	8.795	0.2087	0.622	4.8897	-4.759	5.0703	-0.0362	0.7714	-0.6359	-0.3816	0.7653	1.2356	0.7178	-1.4934	-0.4907	0.3945	0.0117	0.1152	0.4938	0.0312	0.4795	-3.0868	17.2549	12.895
10	4.8549	2.4025	-0.2136	4.3167	5.0589	8.5621	0.0164	0.0391	0.4832	0.1505	0.0242	0.1431	-0.4558	0.3176	0.0073	0.512	-0.0713	-0.0039	0.4417	0.0512	0.3874	11.9138	23.4458	-18.7315
11	9.9483	-2.9932	-3.4416	4.936	-0.4056	4.1399	0.301	-0.4195	-1.8372	-0.0174	-0.1943	-1.7596	1.3941	0.6445	0.0558	0.7218	-0.0052	-0.0378	0.4162	0.0667	1.2068	20.3858	8.0957	-17.6142
12	2.6373	-1.5774	-0.1879	1.8148	2.2825	4.6113	0.0603	-0.0732	-0.2642	0.7306	-0.0787	0.8118	0.4951	-0.284	-0.0015	0.2574	-0.0832	0.0726	0.2424	0.0032	0.2864	12.8595	24.6538	-10.9865
13	9.1399	1.0909	3.3651	8.226	-7.2949	8.5533	0.5621	-0.204	0.5568	0.8241	0.2782	2.701	-0.9218	-0.1674	-0.7427	0.715	0.1101	0.2119	0.4308	0.0614	0.8137	10.2575	45.7115	-7.3413
14	3.2771	0.78	-0.8796	3.3881	0.5059	3.0292	0.5141	-0.0529	0.6976	0.5682	0.1039	-0.224	-0.8113	0.0945	-0.7346	0.5118	-0.0806	0.1307	0.28	-0.0052	0.3933	19.2563	42.0051	-5.3749
15	5.3684	2.7956	-0.1178	8.5755	-4.7436	5.8434	0.0365	0.7633	0.466	-1.3355	0.5227	-0.3746	-1.0402	1.2753	-0.11	0.6261	-0.1843	0.1647	0.4238	-0.0108	0.3042	22.5635	36.0339	-18.046
16	7.7855	0.1992	-3.5663	2.5668	1.7805	3.1665	-0.0346	-0.2866	0.0474	0.9915	0.3748	-0.4706	0.1219	0.9392	-0.3409	0.4226	0.0269	-0.0324	0.3777	-0.0214	0.3265	19.46	25.9699	-3.1083
17	3.4968	-0.6105	2.8484	5.7636	-0.5612	2.4717	0.0449	-0.6974	-0.1685	0.3642	-0.641	-1.3014	0.4447	1.4732	0.1356	0.5106	0.0134	0.0067	0.4797	0.0401	0.4943	24.3951	16.9557	-12.6545
18	3.3754	1.4539	4.1516	2.6641	2.0194	5.3934	0.7306	0.417	0.2612	-0.2034	0.1631	-0.912	0.8566	0.9753	-0.6426	0.3354	-0.0031	0.1091	0.3518	-0.0923	0.5017	22.899	22.9513	-20.2913
19	7.8291	2.2742	-0.9003	6.9212	-2.3416	6.214	-0.2166	0.4936	-0.5144	-0.0777	0.6487	-0.9491	-0.5823	1.8569	-0.1462	0.2431	-0.1329	0.1098	0.4863	-0.1467	0.4393	26.9376	30.0281	-14.74

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN B AND (RESID 2 THROUGH 10 )
2	X-RAY DIFFRACTION	2	CHAIN B AND (RESID 11 THROUGH 26 )
3	X-RAY DIFFRACTION	3	CHAIN B AND (RESID 27 THROUGH 48 )
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESID 49 THROUGH 56 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 57 THROUGH 69 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 70 THROUGH 88 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 89 THROUGH 106 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 107 THROUGH 114 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 115 THROUGH 124 )
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESID 2 THROUGH 10 )
11	X-RAY DIFFRACTION	11	CHAIN A AND (RESID 11 THROUGH 26 )
12	X-RAY DIFFRACTION	12	CHAIN A AND (RESID 27 THROUGH 48 )
13	X-RAY DIFFRACTION	13	CHAIN A AND (RESID 49 THROUGH 56 )
14	X-RAY DIFFRACTION	14	CHAIN A AND (RESID 57 THROUGH 69 )
15	X-RAY DIFFRACTION	15	CHAIN A AND (RESID 70 THROUGH 81 )
16	X-RAY DIFFRACTION	16	CHAIN A AND (RESID 82 THROUGH 94 )
17	X-RAY DIFFRACTION	17	CHAIN A AND (RESID 95 THROUGH 106 )
18	X-RAY DIFFRACTION	18	CHAIN A AND (RESID 107 THROUGH 113 )
19	X-RAY DIFFRACTION	19	CHAIN A AND (RESID 114 THROUGH 124 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi