PDB-4c5e: Crystal structure of the minimal Pho-Sfmbt complex (P21 spacegroup)

ID or keywords:

Entry

Database: PDB / ID: 4c5e

Title

Crystal structure of the minimal Pho-Sfmbt complex (P21 spacegroup)

Components

POLYCOMB PROTEIN PHOPolycomb-group proteins
POLYCOMB PROTEIN SFMBTPolycomb-group proteins

Keywords

TRANSCRIPTION

Function / homology

Function and homology information

SUMOylation of chromatin organization proteins / Transcriptional Regulation by E2F6 / polytene chromosome puff / imaginal disc growth / DNA Damage Recognition in GG-NER / UCH proteinases /

polytene chromosome / PcG protein complex / Ino80 complex / dendrite morphogenesis ...
Similarity search - Function

Biological species

DROSOPHILA MELANOGASTER (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.951 Å

Authors

Alfieri, C. / Glatt, S. / Mueller, C.W.

Citation

Journal: Genes Dev. / Year: 2013
Title: Structural Basis for Targeting the Chromatin Repressor Sfmbt to Polycomb Response Elements
Authors: Alfieri, C. / Gambetta, M.C. / Matos, R. / Glatt, S. / Sehr, P. / Fraterman, S. / Wilm, M. / Mueller, J. / Mueller, C.W.

History

Deposition	Sep 11, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4c5e.cif.gz	765.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4c5e.ent.gz	638.2 KB	Display	PDB format
PDBx/mmJSON format	4c5e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c5/4c5e ftp://data.pdbj.org/pub/pdb/validation_reports/c5/4c5e	HTTPS FTP

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Related structure data

Related structure data	4c5gC 4c5hC 4c5iC 3h6zS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	23308 5okz-4 6kz4-d 3wvr-d 2ba0-d 23307 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	#87 - Mar 2007 Zinc Fingers similarity (6) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (6) #257 - May 2021 Fetal Hemoglobin similarity (6) #122 - Feb 2010 Enhanceosome similarity (4) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: POLYCOMB PROTEIN SFMBT

B: POLYCOMB PROTEIN SFMBT

C: POLYCOMB PROTEIN SFMBT

D: POLYCOMB PROTEIN SFMBT

E: POLYCOMB PROTEIN PHO

F: POLYCOMB PROTEIN PHO

G: POLYCOMB PROTEIN PHO

H: POLYCOMB PROTEIN PHO

219 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	87.510, 147.880, 97.880
Angle α, β, γ (deg.)	90.00, 112.26, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	POLYCOMB PROTEIN SFMBT / Polycomb-group proteins / SCM-LIKE WITH FOUR MBT DOMAIN-CONTAINING PROTEIN 1 / DSFMBT Mass: 51067.664 Da / Num. of mol.: 4 / Fragment: MBT, RESIDUES 531-980 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q9VK33
#2: Protein/peptide	POLYCOMB PROTEIN PHO / Polycomb-group proteins / PROTEIN PLEIOHOMEOTIC / TRANSCRIPTION FACTOR YY1 HOMOLOG Mass: 3630.202 Da / Num. of mol.: 4 / Fragment: SPACER, RESIDUES 145-172 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q8ST83
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1528 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 48.6 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927
Detector	Type: ADSC CCD / Detector: CCD / Date: Jun 16, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.93927 Å / Relative weight: 1
Reflection	Resolution: 1.95→48.6 Å / Num. obs: 166463 / % possible obs: 99.6 % / Observed criterion σ(I): 1.78 / Redundancy: 3.9 % / B_iso Wilson estimate: 28.75 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 11.4
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.85 / Mean I/σ(I) obs: 1.8 / % possible all: 98.4

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H6Z

3h6z

Resolution: 1.951→48.601 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 20.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1976	8325	5 %
R_work	0.1786	-	-
obs	0.1795	166463	99.75 %

Solvent computation

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

Displacement parameters

B_iso mean: 33.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.951→48.601 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14682	0	0	1528	16210

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	15449
X-RAY DIFFRACTION	f_angle_d	0.772	21031
X-RAY DIFFRACTION	f_dihedral_angle_d	10.825	5511
X-RAY DIFFRACTION	f_chiral_restr	0.055	2230
X-RAY DIFFRACTION	f_plane_restr	0.003	2722

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 (%)
1.9512-1.9733	0.2791	269	0.2775	5110	X-RAY DIFFRACTION	97
1.9733-1.9966	0.2672	279	0.2596	5308	X-RAY DIFFRACTION	100
1.9966-2.0209	0.2913	275	0.2504	5212	X-RAY DIFFRACTION	100
2.0209-2.0465	0.2634	277	0.2482	5275	X-RAY DIFFRACTION	100
2.0465-2.0734	0.2552	279	0.2332	5284	X-RAY DIFFRACTION	100
2.0734-2.1018	0.2709	274	0.2193	5217	X-RAY DIFFRACTION	100
2.1018-2.1319	0.2399	279	0.2144	5299	X-RAY DIFFRACTION	100
2.1319-2.1637	0.2274	277	0.211	5260	X-RAY DIFFRACTION	100
2.1637-2.1975	0.2509	277	0.2119	5261	X-RAY DIFFRACTION	100
2.1975-2.2335	0.2455	277	0.209	5285	X-RAY DIFFRACTION	100
2.2335-2.272	0.2195	277	0.1986	5268	X-RAY DIFFRACTION	100
2.272-2.3133	0.2265	278	0.1992	5266	X-RAY DIFFRACTION	100
2.3133-2.3578	0.2249	278	0.1975	5283	X-RAY DIFFRACTION	100
2.3578-2.406	0.2406	277	0.1954	5268	X-RAY DIFFRACTION	100
2.406-2.4583	0.2285	277	0.1936	5266	X-RAY DIFFRACTION	100
2.4583-2.5155	0.2083	278	0.1868	5277	X-RAY DIFFRACTION	100
2.5155-2.5784	0.2132	278	0.1951	5275	X-RAY DIFFRACTION	100
2.5784-2.6481	0.2082	278	0.1816	5286	X-RAY DIFFRACTION	100
2.6481-2.726	0.1982	277	0.1802	5266	X-RAY DIFFRACTION	100
2.726-2.814	0.1935	278	0.1724	5270	X-RAY DIFFRACTION	100
2.814-2.9145	0.181	277	0.1796	5263	X-RAY DIFFRACTION	100
2.9145-3.0312	0.2207	277	0.1823	5276	X-RAY DIFFRACTION	100
3.0312-3.1691	0.1806	279	0.1749	5290	X-RAY DIFFRACTION	100
3.1691-3.3362	0.193	277	0.1733	5275	X-RAY DIFFRACTION	100
3.3362-3.5451	0.1776	279	0.1623	5282	X-RAY DIFFRACTION	100
3.5451-3.8188	0.1631	278	0.1577	5291	X-RAY DIFFRACTION	100
3.8188-4.2029	0.1567	279	0.1458	5295	X-RAY DIFFRACTION	100
4.2029-4.8106	0.1463	278	0.1341	5286	X-RAY DIFFRACTION	100
4.8106-6.059	0.177	280	0.1661	5303	X-RAY DIFFRACTION	100
6.059-48.6159	0.2098	282	0.1799	5341	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	1.4088	-0.361	-1.3313	1.7111	0.2384	2.9002	0.0866	0.267	0.1332	-0.2533	-0.0193	0.1846	-0.2195	-0.3652	-0.0658	0.1539	0.0126	-0.0394	0.1505	0.0228	0.1757	39.2768	-23.7291	7.0491
2	2.7775	0.3157	-1.0798	0.6379	-0.324	3.5	-0.1439	0.0843	-0.2677	0.0388	0.0395	0.234	0.1908	-0.5714	0.1104	0.1143	-0.0128	0.0148	0.1998	-0.016	0.2762	11.6679	-35.2257	32.9475
3	1.2589	0.3465	-0.4762	1.4156	-0.1931	2.6137	-0.0067	-0.2861	-0.0792	0.2787	0.0631	0.0861	-0.1826	-0.1105	-0.0562	0.1381	0.0651	-0.006	0.206	0.0017	0.1704	25.0222	-24.0991	44.8226
4	1.8239	0.5019	-1.0388	1.3951	-0.2622	2.6731	0.1524	-0.5838	0.2711	0.3015	0.0031	-0.1576	-0.3871	0.3196	-0.1395	0.2056	-0.0082	-0.0216	0.3529	-0.1012	0.2548	55.2862	-22.7088	46.1713
5	1.3271	-0.4554	0.1369	0.7605	-0.0139	1.4643	0.0215	0.0918	0.0818	-0.1259	0.0159	-0.1297	-0.1426	0.2475	-0.0288	0.1161	-0.0686	0.0163	0.1857	-0.0252	0.1911	73.6097	-29.1679	12.4375
6	0.9737	0.6541	-1.334	1.7245	0.0452	4.5234	0.014	0.0903	0.0218	0.2409	0.0514	0.3482	0.1736	-0.3451	-0.0597	0.2449	0.0065	0.0454	0.1659	0.086	0.3384	28.0022	-67.4306	37.604
7	1.0059	-0.3952	-0.2897	1.2242	-0.2479	1.5653	-0.0363	0.1722	-0.1614	-0.2945	0.0404	0.0788	0.0474	-0.1665	-0.0125	0.2486	-0.0498	-0.0047	0.1497	-0.0426	0.2001	35.634	-63.5283	-0.3261
8	0.9887	0.1538	-0.4265	1.0481	-0.3669	3.2711	-0.1246	-0.0403	-0.3845	-0.08	0.0621	-0.306	0.5973	0.4426	0.0644	0.2785	0.0877	0.0084	0.2055	-0.0241	0.3712	65.2215	-68.4428	17.6517
9	1.2138	-0.0424	-0.1659	0.7237	0.3358	2.058	-0.0085	-0.5161	-0.23	0.3464	-0.0398	-0.1055	0.2127	0.4512	0.0383	0.3678	0.0227	-0.0594	0.4291	0.1303	0.2811	57.7661	-62.4713	55.5324
10	2.0005	-1.705	-0.0609	2.0002	-4.8788	4.6733	0.2661	-0.5806	-0.811	1.2683	-0.0528	1.0301	0.1005	-0.2116	-0.2165	0.4125	-0.0372	0.1158	0.257	-0.0174	0.4648	48.0915	-49.3013	17.4166
11	2.8919	-1.9039	2.8412	6.4768	-6.2511	6.465	0.0676	0.3327	-0.2181	-0.5692	0.0802	0.1393	0.2995	0.137	-0.1521	0.2863	0.0032	0.0168	0.1575	-0.0472	0.1535	45.9114	-36.1421	-0.4616
12	3.9356	-1.2631	3.3128	3.285	-0.8007	6.2046	0.1009	0.2549	-0.3042	-0.3935	0.0665	0.1148	0.7871	-0.084	-0.1693	0.1509	-0.0345	-0.0192	0.1061	-0.0229	0.1407	47.642	-36.1894	2.3655
13	2.0002	1.7431	-1.7016	6.1778	5.0391	6.3637	-0.2093	0.3568	-1.696	-1.4713	-0.0019	-0.8207	1.123	0.5635	0.2072	0.4651	0.0627	0.1158	0.3445	0.0238	0.6502	45.8164	-48.8973	37.1356
14	2.3106	1.5641	3.2076	4.4979	4.7586	6.4016	0.1369	-0.4509	-0.0373	0.678	-0.0675	-0.247	0.4233	-0.0017	-0.0701	0.3329	0.0044	-0.0195	0.4364	0.057	0.2371	48.1154	-34.6994	54.4822
15	1.8967	2.0791	4.134	2.9576	3.1257	2.0003	0.1596	-0.6108	-0.2751	0.5203	0.1527	-0.3797	0.63	0.1363	-0.3159	0.228	0.0335	-0.0763	0.3712	0.0366	0.1819	46.3981	-34.7658	51.5961
16	5.4723	3.8699	-0.7928	4.2968	-3.1806	4.515	-0.2672	0.4761	1.2172	-0.5384	0.1712	0.1694	-1.0144	-0.0301	0.0958	0.5462	-0.0365	-0.0679	0.2509	0.0763	0.4162	41.6422	-41.6277	35.3913
17	9.1156	5.4644	-5.4288	3.5974	-3.0297	4.4516	-0.0567	-0.195	0.5052	0.4309	0.1505	0.8899	0.0157	-0.1055	-0.0919	0.4384	0.0327	0.1786	0.203	0.0466	0.4894	28.3861	-54.9519	47.7736
18	9.5864	0.8502	-4.1201	1.4588	1.4473	4.1445	0.0987	0.0335	0.8578	0.5395	0.1434	0.7277	-0.3415	-0.1337	-0.2462	0.3787	0.0123	0.1512	0.1432	0.0517	0.443	31.5378	-55.0614	46.7255
19	4.5528	-5.0535	-0.6042	9.2897	4.3036	5.2874	-0.3026	-0.5293	1.3057	0.9259	0.2947	-0.2239	-1.0564	-0.0282	0.0044	0.4811	0.0758	-0.0751	0.2451	-0.0587	0.4626	52.5728	-42.2569	18.8626
20	2.0045	-3.5205	-5.508	5.1056	2.2088	7.3741	-0.0928	0.2422	0.2931	-0.101	0.1408	-0.6721	0.0154	0.3483	-0.0554	0.2179	-0.0334	-0.0212	0.2474	-0.097	0.296	65.461	-56.3119	7.0874
21	7.8338	-1.2273	-9.1692	3.7064	-1.2311	2.0023	0.1108	-0.1395	0.3122	-0.1224	0.1316	-0.5611	-0.2782	0.4806	-0.2381	0.1787	0.0089	0.0175	0.2662	-0.0759	0.295	62.2938	-56.2237	8.1844

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 534 THROUGH 674 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 675 THROUGH 776 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 777 THROUGH 980 )
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESID 532 THROUGH 674 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 675 THROUGH 977 )
6	X-RAY DIFFRACTION	6	CHAIN C AND (RESID 534 THROUGH 674 )
7	X-RAY DIFFRACTION	7	CHAIN C AND (RESID 675 THROUGH 980 )
8	X-RAY DIFFRACTION	8	CHAIN D AND (RESID 534 THROUGH 674 )
9	X-RAY DIFFRACTION	9	CHAIN D AND (RESID 675 THROUGH 977 )
10	X-RAY DIFFRACTION	10	CHAIN E AND (RESID 141 THROUGH 147 )
11	X-RAY DIFFRACTION	11	CHAIN E AND (RESID 148 THROUGH 159 )
12	X-RAY DIFFRACTION	12	CHAIN E AND (RESID 160 THROUGH 170 )
13	X-RAY DIFFRACTION	13	CHAIN F AND (RESID 141 THROUGH 147 )
14	X-RAY DIFFRACTION	14	CHAIN F AND (RESID 148 THROUGH 159 )
15	X-RAY DIFFRACTION	15	CHAIN F AND (RESID 160 THROUGH 170 )
16	X-RAY DIFFRACTION	16	CHAIN G AND (RESID 141 THROUGH 147 )
17	X-RAY DIFFRACTION	17	CHAIN G AND (RESID 148 THROUGH 159 )
18	X-RAY DIFFRACTION	18	CHAIN G AND (RESID 160 THROUGH 170 )
19	X-RAY DIFFRACTION	19	CHAIN H AND (RESID 141 THROUGH 147 )
20	X-RAY DIFFRACTION	20	CHAIN H AND (RESID 148 THROUGH 159 )
21	X-RAY DIFFRACTION	21	CHAIN H AND (RESID 160 THROUGH 170 )

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