PDB-4p0t: Crystal structure of human centromere protein M

ID or keywords:

Entry

Database: PDB / ID: 4p0t

Title

Crystal structure of human centromere protein M

Components

Centromere protein M

Keywords

CELL CYCLE / Mitosis / Kinetochore / CCAN / G-protein

Function / homology

Function and homology information

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

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.493 Å

Authors

Basilico, F. / Pasqualato, S. / Musacchio, A.

Citation

Journal: Elife / Year: 2014
Title: The pseudo GTPase CENP-M drives human kinetochore assembly.
Authors: Basilico, F. / Maffini, S. / Weir, J.R. / Prumbaum, D. / Rojas, A.M. / Zimniak, T. / De Antoni, A. / Jeganathan, S. / Voss, B. / van Gerwen, S. / Krenn, V. / Massimiliano, L. / Valencia, A. ...

History

Deposition	Feb 22, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 9, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 23, 2014	Group: Database references
Revision 1.2	May 8, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4p0t.cif.gz	136.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4p0t.ent.gz	107.2 KB	Display	PDB format
PDBx/mmJSON format	4p0t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4p0t_validation.pdf.gz	442.4 KB	Display	wwPDB validaton report
Full document	4p0t_full_validation.pdf.gz	444 KB	Display
Data in XML	4p0t_validation.xml.gz	15.9 KB	Display
Data in CIF	4p0t_validation.cif.gz	23.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p0/4p0t ftp://data.pdbj.org/pub/pdb/validation_reports/p0/4p0t	HTTPS FTP

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Related structure data

Similar structure data	4n0p-1 2b7k-1 5rue-1 7kxb-d 5rsy-1 5rt7-1 2b7k-3 5s3m-1 3q85-1 5ru8-1 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

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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) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Centromere protein M

B: Centromere protein M

hetero molecules

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

1

A: Centromere protein M

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

2

B: Centromere protein M

hetero molecules

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

Unit cell

Length a, b, c (Å)	104.030, 104.030, 33.560
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	143
Space group name H-M	P3

Components on special symmetry positions

ID	Model	Components
1	1	A-206- HOH

#1: Protein	Centromere protein M / CENP-M / Interphase centromere complex protein 39 / Proliferation-associated nuclear element protein 1 Mass: 19245.443 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPM, C22orf18, ICEN39, PANE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSP4
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.84 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM bicine pH 8.5, 11 % MPD, 8 mM spermidine

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.92 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 0.92 / Wavelength: 0.92 Å
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection twin	Operator: -h,-k,l / Fraction: 0.489
Reflection	Resolution: 1.49→52.25 Å / Num. obs: 64606 / % possible obs: 98.3 % / Redundancy: 9.4 % / Net I/σ(I): 26.3
Reflection shell	Resolution: 1.49→1.54 Å / Redundancy: 8.8 % / R_merge(I) obs: 0.361 / Mean I/σ(I) obs: 6.4 / % possible all: 96.3

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.7.3_928)	refinement
PHENIX		phasing
Coot		model building
xia2	0.3.3.1	data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.493→52.015 Å / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 15.82 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.1636	4808	7.44 %
R_work	0.1243	-	-
obs	0.1268	64606	97.95 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 59.848 Å² / k_sol: 0.369 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.493→52.015 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2280	0	6	297	2583

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2354
X-RAY DIFFRACTION	f_angle_d	0.854	3197
X-RAY DIFFRACTION	f_dihedral_angle_d	13.857	850
X-RAY DIFFRACTION	f_chiral_restr	0.05	398
X-RAY DIFFRACTION	f_plane_restr	0.003	397

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 (%)
1.4937-1.5195	0.2303	214	0.2055	2771	X-RAY DIFFRACTION	83
1.5195-1.5471	0.2018	252	0.194	2982	X-RAY DIFFRACTION	91
1.5471-1.5768	0.2055	244	0.1824	2952	X-RAY DIFFRACTION	90
1.5768-1.609	0.212	248	0.1764	3004	X-RAY DIFFRACTION	89
1.609-1.644	0.1671	242	0.1735	2971	X-RAY DIFFRACTION	92
1.644-1.6822	0.1873	236	0.1812	2992	X-RAY DIFFRACTION	89
1.6822-1.7242	0.1932	234	0.1743	3003	X-RAY DIFFRACTION	93
1.7242-1.7708	0.1762	236	0.1614	2979	X-RAY DIFFRACTION	89
1.7708-1.8229	0.1497	242	0.1619	3038	X-RAY DIFFRACTION	93
1.8229-1.8817	0.1807	240	0.1588	2940	X-RAY DIFFRACTION	90
1.8817-1.9489	0.1568	236	0.1527	3039	X-RAY DIFFRACTION	93
1.9489-2.0269	0.1529	245	0.1536	3016	X-RAY DIFFRACTION	91
2.0269-2.119	0.1743	236	0.1479	3011	X-RAY DIFFRACTION	91
2.119-2.2306	0.1468	254	0.136	3035	X-RAY DIFFRACTION	92
2.2306-2.3702	0.1708	240	0.1305	3026	X-RAY DIFFRACTION	92
2.3702-2.5529	0.1571	242	0.1272	3007	X-RAY DIFFRACTION	92
2.5529-2.8092	0.1723	240	0.1189	3048	X-RAY DIFFRACTION	92
2.8092-3.2144	0.176	227	0.1058	3044	X-RAY DIFFRACTION	93
3.2144-4.0447	0.142	244	0.0722	3053	X-RAY DIFFRACTION	92
4.0447-20.5591	0.1474	248	0.0798	2875	X-RAY DIFFRACTION	88

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	3.8924	0.5815	0.3647	4.0042	1.8529	4.425	-0.0028	0.2175	0.176	-0.1607	0.01	0.2423	-0.1227	-0.2327	-0.0672	0.0509	0.0206	-0.0097	0.1243	0.0168	0.0879	60.8336	81.0864	-0.0726
2	3.1381	-0.2337	-0.3367	4.8651	0.9825	4.805	0.0118	-0.0883	-0.2704	0.1446	-0.014	0.4452	0.3093	-0.0778	0.0582	0.0693	0.0061	-0.0064	0.0997	0.0344	0.1297	61.4376	77.8614	7.0353
3	1.2768	-0.4973	-0.1403	2.0167	-0.3528	2.7393	0.0716	0.04	0.0303	-0.033	0.0111	-0.0632	-0.1924	-0.0173	-0.0676	0.1025	0.0313	0.0024	0.0866	-0.0083	0.0699	69.3081	91.2735	2.3042
4	1.9646	-0.0208	0.5771	2.847	0.1605	4.9332	0.0055	-0.0807	0.1553	-0.0735	-0.0019	-0.2877	-0.2753	0.1361	-0.0632	0.0874	0.0252	0.0103	0.0921	-0.0284	0.1118	74.8028	91.4827	-1.7983
5	2.8797	-1.9675	2.8998	2.4676	-2.6689	7.0857	-0.0087	0.1862	-0.1278	-0.008	-0.0553	-0.043	0.0488	0.2959	-0.0094	0.0601	0.0245	0.0125	0.0833	-0.0009	0.0671	73.1144	74.4192	1.3403
6	4.2051	0.3591	-1.4387	2.4786	-1.9536	4.5722	-0.0372	0.2412	-0.2632	-0.0889	-0.0512	-0.0179	0.0422	0.1224	0.0438	0.0396	0.0249	-0.0006	0.1046	-0.015	0.0802	97.6189	70.9125	-13.5321
7	2.654	-0.6241	-0.3636	6.1803	-0.0673	4.7393	0.1838	0.0536	0.4438	-0.2159	-0.0918	-0.5724	-0.9043	0.1628	-0.0197	0.1983	-0.0134	0.0664	0.132	-0.0155	0.1835	99.2337	79.6954	-10.3604
8	3.9577	-1.2989	0.4361	6.6743	-0.6578	3.8129	0.0585	-0.2699	0.0933	0.4423	0.0853	-0.575	0.0412	0.2121	-0.1244	0.1054	-0.0259	-0.0018	0.1827	-0.0179	0.0359	95.8114	68.2786	-1.8427
9	1.176	-0.3848	-0.1915	2.7378	1.5024	3.7575	0.0887	0.0049	-0.1262	0.0044	-0.0546	-0.0709	0.2804	-0.0736	-0.0571	0.1006	0.0217	-0.0124	0.102	0.0067	0.0583	88.7963	59.9247	-10.2422
10	1.0709	-0.1348	-0.78	1.8569	1.073	5.0109	-0.0254	-0.0464	0.0166	0.0579	0.0296	0.0425	0.0701	-0.0517	-0.0734	0.0883	0.0687	0.0216	0.1026	0.0042	0.0538	84.9324	66.5978	-12.3416
11	4.2612	-1.0767	-2.7173	7.3784	3.8423	3.4747	-0.0085	-0.0172	-0.0058	0.0714	-0.1445	0.3021	0.4329	-0.4232	0.2347	0.133	0.0344	0.022	0.1577	0.0241	0.0894	78.5148	60.2831	-14.5223
12	2.4413	1.6566	-1.8854	2.6486	-1.5468	5.9758	-0.0968	-0.0214	-0.0958	-0.1021	-0.0935	0.0716	0.0526	0.0562	0.086	0.0837	0.0577	0.0144	0.131	0.0157	0.0265	85.0674	68.6542	-16.5754
13	0.6772	-0.8617	-1.0462	5.0154	4.2805	4.197	-0.0081	0.2126	0.2056	-0.2558	-0.0852	0.2069	-0.4141	-0.1154	0.1314	0.0735	0.0172	-0.023	0.1331	0.0149	0.0908	90.2931	79.0845	-16.1008
14	1.9985	0.0286	0.1538	2.1275	0.0288	0.396	-0.0002	-0.0449	0.4775	0.0741	0.0017	-0.0167	-0.167	-0.0506	-0.0894	0.2382	0.1255	-0.0138	0.1405	-0.098	0.4666	85.8363	87.163	-4.1087
15	2.3012	-0.4099	-1.3642	2.7056	0.9397	4.9063	0.1055	0.0243	0.147	0.005	-0.087	0.3192	-0.3581	-0.4454	0.0858	0.1954	0.119	-0.0287	0.1968	-0.0743	0.1301	78.373	78.4195	-8.4534

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 20:41)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 42:69)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 70:115)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 116:140)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 141:167)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 20:41)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 42:54)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 61:69)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 70:92)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 93:115)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 116:128)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 129:140)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 141:159)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 160:166)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 167:170)

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