PDB-5z08: The crystal structure of kinetochore subunits Cenp-H/I/K triple c...

ID or keywords:

Entry

Database: PDB / ID: 5z08

Title

The crystal structure of kinetochore subunits Cenp-H/I/K triple complex

Components

Cenp-H
Cenp-I
Cenp-K

Keywords

CELL CYCLE /

protein complex /

kinetochore /

centromere

Function / homology

Function and homology information

kinetochore => GO:0000776 / centromere complex assembly /

kinetochore assembly /

chromosome, centromeric region /

kinetochore /

nucleus
Similarity search - Function

Biological species

Chaetomium thermophilum (fungus)

Thielavia terrestris (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.199 Å

Authors

Tian, W. / Hu, L.Q. / He, X.

Funding support

China, 3items

Organization	Grant number	Country
National Natural Science Foundation of China	31500629	China
National Natural Science Foundation of China	31470763	China
National Natural Science Foundation of China	31500605	China

Citation

Journal: Nucleic Acids Res. / Year: 2019
Title: Structural analysis of fungal CENP-H/I/K homologs reveals a conserved assembly mechanism underlying proper chromosome alignment.
Authors: Hu, L. / Huang, H. / Hei, M. / Yang, Y. / Li, S. / Liu, Y. / Dou, Z. / Wu, M. / Li, J. / Wang, G.Z. / Yao, X. / Liu, H. / He, X. / Tian, W.

History

Deposition	Dec 18, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 31, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Mar 27, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5z08.cif.gz	246.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5z08.ent.gz	200.5 KB	Display	PDB format
PDBx/mmJSON format	5z08.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z0/5z08 ftp://data.pdbj.org/pub/pdb/validation_reports/z0/5z08	HTTPS FTP

-
Related structure data

Related structure data	5z07C C: citing same article (ref.)
Similar structure data	6pfq-d 5wtd-d 6mcq-2 4d8m-d 4yqx-d 6ejd-d 3h8l-d 2x8g-d 6rtm-d 4hn0-d 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

Deposited unit

A: Cenp-I

B: Cenp-I

C: Cenp-K

D: Cenp-H

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	67.847, 67.847, 186.269
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

#1: Protein	Cenp-I Mass: 25791.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0061880 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SFF7
#2: Protein	Cenp-K Mass: 18868.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thielavia terrestris (strain ATCC 38088 / NRRL 8126) (fungus) Strain: ATCC 38088 / NRRL 8126 / Gene: THITE_2065850 / Production host: Escherichia coli (E. coli) / References: UniProt: G2R3T1
#3: Protein/peptide	Cenp-H Mass: 5200.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thielavia terrestris (strain ATCC 38088 / NRRL 8126) (fungus) Strain: ATCC 38088 / NRRL 8126 / Gene: THITE_2113209 / Production host: Escherichia coli (E. coli) / References: UniProt: G2R207
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 56.59 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 8000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.986 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 15, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.986 Å / Relative weight: 1
Reflection	Resolution: 2.199→50 Å / Num. obs: 42600 / % possible obs: 100 % / Redundancy: 9.4 % / Net I/σ(I): 29.6
Reflection shell	Resolution: 2.2→2.24 Å

-
Processing

Software

Name	Version	Classification
PHENIX	(dev_2463)	refinement
PHASER		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.199→47.975 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.49

	R_factor	Num. reflection	% reflection
R_free	0.2298	2143	5.04 %
R_work	0.1877	-	-
obs	0.1898	42479	99.74 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.199→47.975 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4579	0	0	120	4699

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4669
X-RAY DIFFRACTION	f_angle_d	0.901	6325
X-RAY DIFFRACTION	f_dihedral_angle_d	10.28	1720
X-RAY DIFFRACTION	f_chiral_restr	0.05	728
X-RAY DIFFRACTION	f_plane_restr	0.006	809

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 (%)
2.1988-2.2499	0.3843	148	0.3172	2611	X-RAY DIFFRACTION	98
2.2499-2.3062	0.3265	158	0.2906	2681	X-RAY DIFFRACTION	100
2.3062-2.3685	0.3111	139	0.252	2667	X-RAY DIFFRACTION	100
2.3685-2.4382	0.3032	127	0.2507	2709	X-RAY DIFFRACTION	100
2.4382-2.5169	0.2705	158	0.2366	2691	X-RAY DIFFRACTION	100
2.5169-2.6069	0.2756	133	0.2082	2696	X-RAY DIFFRACTION	100
2.6069-2.7112	0.3067	163	0.2174	2668	X-RAY DIFFRACTION	100
2.7112-2.8346	0.241	159	0.2082	2664	X-RAY DIFFRACTION	100
2.8346-2.9841	0.2812	157	0.2198	2663	X-RAY DIFFRACTION	100
2.9841-3.171	0.2969	134	0.2131	2714	X-RAY DIFFRACTION	100
3.171-3.4158	0.2472	143	0.2009	2690	X-RAY DIFFRACTION	100
3.4158-3.7594	0.223	150	0.1775	2691	X-RAY DIFFRACTION	100
3.7594-4.3031	0.1929	122	0.1611	2724	X-RAY DIFFRACTION	100
4.3031-5.4202	0.1673	113	0.1538	2728	X-RAY DIFFRACTION	100
5.4202-47.9865	0.1819	139	0.1632	2739	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	7.5665	-1.0038	2.7986	3.4348	0.629	4.8797	0.042	0.6161	0.2278	-0.5875	0.0457	-0.0351	-0.8432	0.4239	-0.0463	0.7878	-0.0594	-0.0003	0.3896	0.0293	0.322	63.9626	59.7477	-41.6722
2	7.4521	-4.1078	5.9952	3.0919	-2.1546	9.0863	0.2597	0.512	-0.1746	-0.7059	0.1817	-0.1619	-0.0114	0.576	-0.4732	0.4999	-0.0429	0.0238	0.421	-0.0339	0.3054	71.6973	49.7959	-35.0033
3	3.0854	-0.0655	0.2984	1.6289	0.4479	3.8187	-0.0071	-0.2414	0.1521	-0.1177	0.1087	-0.0326	-0.5429	-0.0827	-0.1129	0.3713	-0.0261	0.0061	0.4409	-0.0017	0.2595	64.9862	59.7587	-21.1349
4	3.0563	-0.2115	-1.119	1.639	0.0545	2.5054	-0.0545	-1.1561	0.0208	0.2816	-0.0244	-0.017	-0.1204	-0.2656	0.059	0.4724	0.0227	-0.0177	1.0581	0.0173	0.3413	57.1885	56.579	-2.0378
5	3.4653	-0.4753	-1.1241	2.6232	2.3636	3.134	-0.1809	-1.0657	-0.2993	1.4879	-0.184	0.1073	0.1344	-0.1834	0.3564	1.1349	-0.0181	0.0565	0.8988	0.0112	0.3774	61.7172	50.6141	0.1043
6	3.8116	5.1057	-0.5938	6.9311	-0.2544	3.4266	-0.1249	-0.0736	-1.0368	0.1236	0.3271	-0.9104	0.2212	0.8078	-0.2198	0.3946	0.0705	-0.0509	0.6394	-0.0866	0.4318	79.6804	47.3849	-20.4414
7	2.3945	1.2036	1.8638	4.4645	0.4301	2.1939	0.3546	-3.0816	0.3678	0.858	-1.0219	0.0379	-0.2861	1.3357	0.548	0.7176	-0.139	0.0653	1.1724	0.0197	0.4243	91.5024	50.2537	12.6595
8	4.6025	0.7849	2.9655	2.3311	0.6716	4.1666	0.0514	-1.3509	-0.6642	0.5089	-0.5044	-0.4541	0.0849	0.0557	0.3456	0.6546	-0.0761	0.0334	0.9474	0.2543	0.4746	94.9296	42.9264	9.9627
9	3.0719	0.8112	-0.2944	2.1652	0.1245	2.1709	0.0638	-1.0845	-0.1443	0.2369	-0.2677	-0.0708	-0.073	0.5676	0.1686	0.4694	0.0177	0.0062	0.8496	0.0411	0.3235	95.9081	51.5841	3.2004
10	2.4755	0.0441	-0.6387	1.1281	-0.3038	1.9267	-0.0474	-0.088	0.1178	-0.0289	-0.0667	-0.0501	-0.2118	0.1455	0.0894	0.404	0.0026	0.01	0.6289	-0.0304	0.2907	96.0279	58.363	-7.7772
11	8.1878	-0.7125	0.4056	3.6265	-0.8776	4.8721	-0.3981	-0.1434	-0.0202	-0.2804	0.0954	-0.2318	-0.1695	-0.1779	0.3027	0.3719	0.0162	0.0406	0.6316	0.0114	0.2848	102.9399	56.5238	-16.6302
12	5.8172	-0.436	-1.534	1.5957	0.3994	2.0546	-0.0162	1.1027	0.2109	-0.2611	0.0972	0.1244	-0.2217	-0.0906	-0.0806	0.5316	0.0194	0.0063	0.7838	0.0731	0.3151	103.8858	62.877	-25.6031
13	2.9728	1.1093	-2.4377	1.8708	-2.8677	4.7961	-0.1873	1.0415	-0.1437	-1.7014	0.1149	0.1433	0.002	-0.3112	0.3187	1.0664	0.0642	0.0619	1.0204	-0.1338	0.3957	98.5598	56.2873	-27.051
14	4.9669	-3.4729	-4.4425	5.5114	1.5768	6.2912	-0.2762	0.816	-1.6065	-0.4719	-0.0188	0.5267	0.4953	-0.2972	0.152	0.381	-0.0029	-0.0237	0.6165	-0.0709	0.4125	81.2851	45.0577	-9.5576
15	3.9717	-1.2369	-0.7025	5.4792	-0.6658	3.2608	0.1632	-0.2059	1.2056	0.2857	-0.0254	0.4066	-1.2516	0.0448	-0.1757	0.9401	0.0278	0.1264	0.6917	-0.1776	0.9453	98.5652	85.7247	-8.2978
16	4.3103	-0.0308	-0.6515	4.3672	0.6174	5.4749	0.3535	-0.0706	1.0419	-0.4709	-0.0049	-0.2979	-0.4581	0.6234	-0.3659	1.0031	-0.2091	0.1302	0.7212	-0.0607	0.9953	116.0356	82.5883	-10.7214
17	4.3799	-0.2378	0.6208	5.0441	0.2749	6.8998	0.3578	0.134	0.8968	-0.4744	-0.1988	-0.2572	-0.2878	0.8119	-0.008	0.837	-0.1527	0.196	0.7842	-0.0306	0.7312	114.2659	75.8732	-17.8743
18	4.9415	-2.7959	1.7652	9.2442	-5.0663	4.8726	0.3304	0.1702	0.9296	-1.0567	-0.0184	0.1729	0.0624	-0.058	-0.2703	0.8017	-0.0686	0.0273	0.7243	-0.0389	0.621	100.133	82.609	-16.9421
19	5.3027	-1.3007	1.2356	7.2731	-3.1843	2.7467	0.4287	-0.8666	0.558	0.7136	-0.3104	0.1295	-0.4399	0.0604	-0.1497	0.5433	-0.0151	0.0898	0.7189	-0.0829	0.361	97.6018	72.1111	-2.9593

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 45 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 46 through 137 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 138 through 191 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 192 through 212 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 213 through 229 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 8 through 21 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 22 through 45 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 46 through 76 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 77 through 137 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 138 through 154 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 155 through 191 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 192 through 212 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 213 through 229 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 161 through 183 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 184 through 295 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 296 through 328 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 184 through 209 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 210 through 227 )

-
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://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