PDB-3b0d: Crystal structure of the chicken CENP-T histone fold/CENP-W compl...

ID or keywords:

Entry

Database: PDB / ID: 3b0d

Title

Crystal structure of the chicken CENP-T histone fold/CENP-W complex, crystal form II

Components

Centromere protein T
Centromere protein W

Keywords

DNA BINDING PROTEIN /

histone fold /

DNA binding

Function / homology

Function and homology information

Mitotic Prometaphase / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / Deposition of new CENPA-containing nucleosomes at the centromere /

kinetochore assembly /

chromosome segregation /

kinetochore ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.197 Å

Authors

Nishino, T. / Takeuchi, K. / Gascoigne, K.E. / Suzuki, A. / Hori, T. / Oyama, T. / Morikawa, K. / Cheeseman, I.M. / Fukagawa, T.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2012
Title: CENP-T-W-S-X Forms a Unique Centromeric Chromatin Structure with a Histone-like Fold.
Authors: Nishino, T. / Takeuchi, K. / Gascoigne, K.E. / Suzuki, A. / Hori, T. / Oyama, T. / Morikawa, K. / Cheeseman, I.M. / Fukagawa, T.

History

Deposition	Jun 8, 2011	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 7, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2017	Group: Refinement description / Category: software
Revision 1.2	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3b0d.cif.gz	154.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3b0d.ent.gz	125 KB	Display	PDB format
PDBx/mmJSON format	3b0d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b0/3b0d ftp://data.pdbj.org/pub/pdb/validation_reports/b0/3b0d	HTTPS FTP

-
Related structure data

Related structure data	3b0bC 3b0cC 3vh5C 3vh6C C: citing same article (ref.)
Similar structure data	4z82-d 3cou-d 6yro-5 2gh2-d 2ka4-d 4kwk-d 4xez-d 4iey-d 4ubh-d 3ici-1 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	#7 - Jul 2000 Nucleosome similarity (2) #241 - Jan 2020 Twenty Years of Molecules similarity (2)

Deposited unit

T: Centromere protein T

W: Centromere protein W

B: Centromere protein T

C: Centromere protein W

hetero molecules

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

1

T: Centromere protein T

W: Centromere protein W

hetero molecules

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

2

B: Centromere protein T

C: Centromere protein W

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.985, 54.985, 235.912
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Centromere protein T / / CENP-T Mass: 12746.921 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 54-162 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENPT / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F1NPG5
#2: Protein	Centromere protein W / / CENP-W Mass: 8708.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENPW / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0DJH6*PLUS
#3: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	SEQUENCE DATABASE REFERENCE FOR THE CHAIN W/C DOES NOT CURRENTLY EXIST.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.73 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100mM Citrate-NaOH pH 5.0, 30% PEG 600, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2011
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.197→40.732 Å / Num. all: 22025 / Num. obs: 22025 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell	Resolution: 2.2→2.25 Å / % possible all: 100

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER	in PHENIX package	phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.197→40.732 Å / SU ML: 0.63 / σ(F): 1.34 / Phase error: 25.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2609	2011	9.14 %	random
R_work	0.2026	-	-	-
obs	0.2078	21997	99.51 %	-
all	-	22105	-	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 53.733 Å² / k_sol: 0.334 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.1288 Å²	-0 Å²	0 Å²
2-	-	-0.1288 Å²	-0 Å²
3-	-	-	0.2577 Å²

Refinement step

Cycle: LAST / Resolution: 2.197→40.732 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2775	0	52	125	2952

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2874
X-RAY DIFFRACTION	f_angle_d	1.078	3860
X-RAY DIFFRACTION	f_dihedral_angle_d	13.834	1120
X-RAY DIFFRACTION	f_chiral_restr	0.075	445
X-RAY DIFFRACTION	f_plane_restr	0.005	482

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 (%)
2.1967-2.2517	0.3032	137	0.2588	1364	X-RAY DIFFRACTION	100
2.2517-2.3125	0.3208	143	0.2281	1417	X-RAY DIFFRACTION	100
2.3125-2.3806	0.3369	145	0.2439	1426	X-RAY DIFFRACTION	100
2.3806-2.4574	0.3305	135	0.2479	1356	X-RAY DIFFRACTION	100
2.4574-2.5452	0.3328	142	0.2382	1431	X-RAY DIFFRACTION	100
2.5452-2.6471	0.2785	142	0.2298	1431	X-RAY DIFFRACTION	100
2.6471-2.7676	0.3347	145	0.2153	1401	X-RAY DIFFRACTION	100
2.7676-2.9134	0.2997	145	0.2334	1417	X-RAY DIFFRACTION	100
2.9134-3.0959	0.2876	137	0.2368	1437	X-RAY DIFFRACTION	100
3.0959-3.3349	0.3057	144	0.2284	1412	X-RAY DIFFRACTION	100
3.3349-3.6703	0.2534	154	0.2005	1473	X-RAY DIFFRACTION	100
3.6703-4.2009	0.2157	147	0.175	1438	X-RAY DIFFRACTION	100
4.2009-5.2909	0.2168	144	0.1511	1455	X-RAY DIFFRACTION	99
5.2909-40.7395	0.2282	151	0.2012	1528	X-RAY DIFFRACTION	95

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	0.0066	0	0.0054	0.0009	0.0042	0.0079	0.0505	-0.0138	-0.0582	0.0189	0.099	0.0569	0.0936	0.0004	0.0001	0.6809	0.1496	0.0445	0.467	-0.0106	0.3819	18.6046	-3.0621	48.5189
2	0.0604	-0.089	-0.0292	0.0979	0.041	0.0172	-0.2065	-0.2296	0.1922	0.0424	-0.021	0.2966	0.0857	-0.0141	-0.0886	0.5156	0.5884	-0.1963	-0.0538	-0.3059	0.3198	16.8125	7.1392	39.5444
3	0.0057	-0.0074	-0.0037	0.0036	0.0004	0.0087	-0.075	0.0569	0.0275	-0.0384	-0.0051	0.1012	-0.0434	-0.0362	-0	0.4324	0.1074	-0.0259	0.3404	-0.0182	0.4124	21.0069	3.6607	26.6482
4	-0.0012	-0.0006	0.0054	0.0054	0.0047	0.0076	-0.1502	0.1889	-0.1198	0.0161	-0.0372	-0.0333	0.0385	0.1066	-0.0003	0.3874	0.0184	-0.0073	0.2147	-0.0571	0.3575	27.5886	-4.5632	29.6743
5	0.0063	-0.0039	0.0032	0.002	0.0008	0.0046	-0.0499	0.0576	-0.0574	0.0194	-0.0317	0.0297	0.0489	0.0449	0.0001	0.3885	-0.0567	0.0161	0.4023	-0.1217	0.5337	16.9971	-13.0216	28.5211
6	0.0001	0.0001	-0.0003	0.0013	-0.0009	0.0031	-0.0183	0.0045	-0.009	0.0088	-0.0139	-0.0117	-0.0233	-0.0095	0.0001	1.0719	0.0404	0.0819	1.0266	0.027	1.0078	13.8408	-9.7152	42.4157
7	0.0055	-0.0008	0.0008	0.0002	0.0013	-0.0007	0.0537	0.0084	-0.044	0.0172	0.0354	0.0036	-0.0221	-0.0085	-0.0005	0.479	0.128	0.0112	0.7127	-0.2205	0.7053	7.1292	3.3808	38.1608
8	-0.0006	-0.0013	-0.0008	0.0093	0.0009	0.0006	-0.0142	0.0413	-0.0101	-0.0107	0.0479	0.0112	-0.0072	-0.0866	-0.0001	0.4162	0.1637	-0.108	0.599	-0.2486	0.5842	6.1229	5.4926	29.6386
9	0.0726	0.0295	0.0147	0.0284	0.0017	0.0754	-0.1726	-0.1634	0.0839	0.3832	0.2371	-0.1105	0.0038	0.0363	0.0809	0.4653	0.1872	-0.1238	0.2374	-0.1183	0.3967	27.413	0.9189	45.9527
10	0.0312	0.0107	-0.0033	0.0492	0.0045	0.0011	-0.0903	-0.018	0.0496	-0.0415	0.0439	-0.0159	0.0253	0.0073	0.0044	0.6135	0.1947	-0.2685	0.2528	-0.1187	0.5633	27.4113	10.0494	45.213
11	0.09	0.046	-0.0439	0.0335	-0.0215	0.0187	-0.0904	-0.0475	0.0204	-0.027	-0.0216	0.0312	-0.0692	-0.0171	-0.0055	0.6746	-0.1029	-0.1081	0.3448	-0.1184	0.3422	5.7817	-11.6477	-2.7958
12	0.0102	0.0118	-0.0069	0.0296	0.0142	0.0967	-0.2073	0.1057	-0.0377	0.0582	-0.1703	0.1247	0.029	-0.1348	-0.2038	0.6973	-0.5489	-0.0092	0.3901	-0.1007	0.3062	7.3841	-23.0053	-0.4785
13	0.0093	-0.0098	-0.0019	0.0186	-0.0022	0.0126	-0.0321	-0.0493	0.033	0.0457	-0.0301	-0.0467	0.0875	-0.0208	-0.0183	0.5485	-0.312	0.0852	0.2979	-0.0871	0.3274	14.1453	-25.7734	15.8647
14	0.0019	0.0022	-0.0039	0.0008	-0.0001	0.0039	-0.0321	0.0154	-0.0029	-0.0276	-0.0289	-0.0466	0.0283	0.003	-0.0001	0.5023	-0.1757	0.0633	0.3468	-0.0437	0.5212	24.7609	-18.9389	8.5384
15	0.0046	0.0053	-0.0022	0.0084	-0.008	0.0099	-0.0646	-0.0256	0.0732	-0.0675	0.0032	0.0533	-0.105	-0.0267	-0.0128	0.6136	-0.2503	0.066	0.2997	-0.2943	0.528	15.4729	-8.1665	13.9408
16	0.0127	-0.019	-0.0358	0.1123	0.0766	0.1148	0.0089	-0.108	-0.0199	0.0067	-0.0041	0.0945	0.0005	-0.118	0.0031	0.6563	-0.3803	0.0356	0.7578	-0.1387	0.5114	1.8012	-19.9403	11.1467
17	0.006	-0.0094	-0.015	0.0245	0.0393	0.0378	-0.1376	0.0505	0.0466	-0.3667	-0.066	0.0099	-0.039	-0.047	-0.2711	0.7516	-0.5576	-0.0235	0.0882	-0.1692	0.2788	14.2765	-18.496	-6.391

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN T AND (RESSEQ 535:549)
2	X-RAY DIFFRACTION	2	CHAIN T AND (RESSEQ 550:589)
3	X-RAY DIFFRACTION	3	CHAIN T AND (RESSEQ 590:599)
4	X-RAY DIFFRACTION	4	CHAIN T AND (RESSEQ 600:616)
5	X-RAY DIFFRACTION	5	CHAIN T AND (RESSEQ 617:631)
6	X-RAY DIFFRACTION	6	CHAIN W AND (RESSEQ 2:6)
7	X-RAY DIFFRACTION	7	CHAIN W AND (RESSEQ 7:17)
8	X-RAY DIFFRACTION	8	CHAIN W AND (RESSEQ 18:26)
9	X-RAY DIFFRACTION	9	CHAIN W AND (RESSEQ 27:59)
10	X-RAY DIFFRACTION	10	CHAIN W AND (RESSEQ 60:76)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 535:549)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 550:582)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 583:599)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 600:608)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 609:629)
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESSEQ 2:26)
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESSEQ 27:76)

-
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