PDB-3cey: Crystal structure of L3MBTL2

ID or keywords:

Entry

Database: PDB / ID: 3cey

Title

Crystal structure of L3MBTL2

Components

Lethal(3)malignant brain tumor-like 2 protein

Keywords

TRANSCRIPTION REGULATOR / MBT /

Structural Genomics /

Structural Genomics Consortium / SGC / Chromatin regulator / Metal-binding /

Nucleus /

Transcription /

Transcription regulation /

Zinc-finger

Function / homology

Function and homology information

Transcriptional Regulation by E2F6 / methylated histone binding / SUMOylation of chromatin organization proteins / chromatin organization /

histone binding / negative regulation of DNA-templated transcription /

chromatin binding / zinc ion binding /

nucleoplasm /

nucleus
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Nady, N. / Guo, Y. / Pan, P. / Allali-Hassani, A. / Qi, C. / Zhu, H. / Dong, A. / Mackenzie, F. / Crombet, L. / Loppnau, P. ...

Citation

Journal: Nucleic Acids Res. / Year: 2009
Title: Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.
Authors: Guo, Y. / Nady, N. / Qi, C. / Allali-Hassani, A. / Zhu, H. / Pan, P. / Adams-Cioaba, M.A. / Amaya, M.F. / Dong, A. / Vedadi, M. / Schapira, M. / Read, R.J. / Arrowsmith, C.H. / Min, J.

History

Deposition	Feb 29, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 6, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3cey.cif.gz	169.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3cey.ent.gz	139.5 KB	Display	PDB format
PDBx/mmJSON format	3cey.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	3f70C C: citing same article (ref.)
Similar structure data	6zxt-d 4gmk-d 5tv3-4 4ygf-3 6jgt-d 4o5f-d 6ag0-1 4u0l-2 6bg3-d 4xfw-d 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	#177 - Sep 2014 Apoptosomes similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Lethal(3)malignant brain tumor-like 2 protein

B: Lethal(3)malignant brain tumor-like 2 protein

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

1

A: Lethal(3)malignant brain tumor-like 2 protein

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

2

B: Lethal(3)malignant brain tumor-like 2 protein

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	55.643, 55.938, 329.090
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Lethal(3)malignant brain tumor-like 2 protein / L3 / mbt-like 2 protein / H-l3 / mbt-like protein Mass: 54347.379 Da / Num. of mol.: 2 / Fragment: UNP residues 170-625 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q969R5
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Lethal(3)malignant brain tumor-like 2 protein / L3 / mbt-like 2 protein / H-l3 / mbt-like protein

Mass: 54347.379 Da / Num. of mol.: 2 / Fragment: UNP residues 170-625
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: L3MBTL2 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q969R5

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.36 Å³/Da / Density % sol: 47.79 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 10% PEG 3350, 0.1M NaAcetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2007
Radiation	Monochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→100 Å / Num. all: 47081 / Num. obs: 47081 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→35.91 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.922 / SU B: 12.955 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25207	2391	5.1 %	RANDOM
R_work	0.21006	-	-	-
all	0.21221	44600	-	-
obs	0.21221	44600	87.65 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 35.078 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.3 Å²	0 Å²	0 Å²
2-	-	0.64 Å²	0 Å²
3-	-	-	-1.94 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→35.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6181	0	0	165	6346

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.027	0.022	6367
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.845	1.931	8672
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.256	5	773
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.622	23.06	268
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17	15	972
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.757	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.125	0.2	945
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	4830
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	2483
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.312	0.2	4196
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	273
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.215	0.2	45
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.257	0.2	3
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.995	1.5	4002
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.591	2	6287
X-RAY DIFFRACTION	r_scbond_it	2.523	3	2835
X-RAY DIFFRACTION	r_scangle_it	3.642	4.5	2385
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.199→2.256 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.394	87	-
R_work	0.283	1565	-
obs	-	-	42.21 %

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	5.2869	0.6469	2.0473	2.4405	-0.2926	9.1901	-0.1085	-0.0891	0.3883	-0.0641	0.0513	0.1626	-0.5512	-0.2669	0.0572	0.3926	0.078	0.0223	-0.0263	0.0233	0.141	-0.5204	-8.8801	-64.0503
2	1.7922	-1.0866	0.7923	5.5277	-4.6042	5.4369	-0.0353	0.0473	-0.079	-0.1027	-0.0107	0.1371	-0.0741	0.1599	0.046	0.3141	0.0046	-0.0641	-0.0227	-0.0161	0.103	1.9764	3.9635	-78.1468
3	7.809	-17.7263	3.1198	62.9039	-13.9519	6.4079	-0.0467	-0.0359	0.6589	-0.3026	-0.7966	-1.9143	-0.7439	0.6842	0.8433	0.3193	-0.0418	-0.1858	0.0264	0.0044	0.1186	12.2596	4.5544	-71.9447
4	2.519	0.4961	0.9742	10.4578	-2.6055	4.5784	0.328	0.3582	0.1025	-0.4579	0.023	0.1589	0.7182	0.31	-0.351	0.2748	0.161	-0.0948	-0.0095	-0.0668	0.0817	13.4283	-30.0308	-59.3717
5	3.616	-1.6933	1.4422	3.9492	-1.8246	8.3313	0.1037	0.1278	-0.541	-0.5801	0.1189	0.2058	1.2186	0.5727	-0.2226	0.44	0.1717	-0.0496	0.0045	-0.0511	0.1038	13.9074	-32.3475	-56.4448
6	3.8047	0.7033	-2.2173	3.2043	-0.3251	1.471	-0.214	-0.4018	-0.1439	-0.0767	0.1771	0.1004	0.3656	0.1093	0.037	0.2872	0.0965	0.0488	0.1355	0.0903	0.0742	7.2787	-26.7205	-35.5118
7	2.7492	-3.0678	-0.6685	6.7631	0.8625	4.7815	-0.1689	-0.335	-0.3008	0.2195	0.1432	0.2981	0.7244	-0.1472	0.0257	0.2325	0.0938	-0.0344	0.1052	0.0759	0.1044	9.0693	-28.4841	-38.3265
8	7.0767	-0.1569	-0.8452	4.8987	-3.1643	7.1849	-0.1575	-0.4143	-0.1249	0.179	0.3367	0.4973	-0.0485	-0.2729	-0.1792	0.2036	0.2201	0.0793	0.1473	0.0479	-0.0194	-0.3676	-23.6941	-29.6795
9	3.4036	-0.1878	-0.6571	2.4433	-0.9208	9.1165	0.2359	-0.3157	-0.2845	0.0079	0.0466	0.3549	0.2366	-0.8639	-0.2825	0.1786	-0.0314	-0.0709	0.1585	0.1341	0.1202	-4.7357	-18.1133	-52.7576
10	3.7113	-0.0264	-0.8339	2.0641	0.3448	5.8077	0.1228	-0.0474	-0.0056	-0.1369	0.0232	0.2069	0.4196	-0.1205	-0.1459	0.2931	0.0283	-0.0799	0.0671	0.0094	0.1172	1.331	-17.8458	-60.0891
11	2.1451	-0.9165	-0.991	7.926	0.8834	6.3935	-0.006	0.0658	-0.0443	0.0705	0.1228	0.2739	-0.2645	-0.0438	-0.1168	-0.0479	0.1109	0.0037	0.2379	0.0505	0.0304	14.132	9.3631	-17.7438
12	10.1764	-2.4508	-3.4822	9.3393	9.2201	22.3436	-0.3303	0.3224	-0.2137	-0.1163	0.2909	-0.1279	0.0393	0.2229	0.0394	0.043	-0.0193	0.0129	0.1433	0.0723	0.1417	2.5136	7.2817	-4.9189
13	5.6758	-2.6472	-4.3343	2.9093	1.6781	4.2829	0.1004	-0.0255	0.0117	0.0703	-0.077	0.0296	0.14	-0.073	-0.0233	0.0562	0.0017	-0.0107	0.299	0.0001	0.152	2.4156	10.3806	-4.6422
14	8.7072	-5.5518	-4.9092	5.9901	2.6401	3.6112	-0.5497	-0.1061	-0.8658	0.3434	0.0023	0.3789	0.5869	-0.0629	0.5474	0.0719	-0.0409	0.0261	0.1592	0.0355	0.1018	0.6171	2.7781	-3.836
15	9.7833	-1.722	-4.3631	8.5583	1.3208	18.5598	-0.5166	-0.6807	-0.4943	0.6994	0.254	-0.6328	-0.119	2.2042	0.2626	-0.0591	0.2403	-0.1048	0.3773	0.0524	0.1481	40.4609	-7.2036	-21.2042
16	4.3333	-5.0923	-1.1096	6.11	2.2338	7.1592	-0.383	-0.3982	0.4891	0.5019	0.2474	-0.8126	0.4768	0.9968	0.1356	0.0167	0.2378	-0.0848	0.3487	0.0109	0.2342	35.6949	-4.9579	-18.5317
17	4.0739	-1.0297	-0.416	1.2023	0.9342	7.7519	-0.2342	-0.4394	-0.6356	0.7301	0.1293	-0.0165	0.8925	-0.128	0.105	0.3501	0.3108	0.0996	0.1681	0.0793	0.1837	33.2241	-16.3958	-24.7165
18	2.8593	-1.4701	-1.4262	8.9126	-0.2931	5.5255	-0.0547	0.0342	0.0108	-0.3264	0.1096	-0.4743	0.3388	0.5484	-0.0549	0.1021	0.0909	0.0887	0.2307	-0.014	0.0741	33.7383	-9.1229	-40.4682
19	3.7806	-1.1363	-3.4959	2.6587	1.189	6.7576	0.2893	0.9789	0.153	-0.5128	-0.1943	-0.2677	-0.3173	-0.7398	-0.095	0.1835	0.1153	0.0999	0.246	0.0176	0.0238	27.5274	-4.4733	-48.1554
20	2.4153	-0.5016	-1.3635	2.5871	0.2013	5.1484	0.0499	0.1929	0.1108	-0.2609	-0.0441	-0.3039	-0.0934	0.0019	-0.0058	0.0699	0.0573	0.0129	0.19	0.01	0.1463	21.6261	6.1451	-26.8285

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	172 - 211	21 - 60
2	X-RAY DIFFRACTION	2	A	A	212 - 297	61 - 146
3	X-RAY DIFFRACTION	3	A	A	298 - 314	147 - 163
4	X-RAY DIFFRACTION	4	A	A	315 - 340	164 - 189
5	X-RAY DIFFRACTION	5	A	A	341 - 419	190 - 268
6	X-RAY DIFFRACTION	6	A	A	420 - 450	269 - 299
7	X-RAY DIFFRACTION	7	A	A	451 - 489	300 - 338
8	X-RAY DIFFRACTION	8	A	A	490 - 534	339 - 383
9	X-RAY DIFFRACTION	9	A	A	535 - 579	384 - 428
10	X-RAY DIFFRACTION	10	A	A	580 - 604	429 - 453
11	X-RAY DIFFRACTION	11	B	B	173 - 207	22 - 56
12	X-RAY DIFFRACTION	12	B	B	208 - 230	57 - 79
13	X-RAY DIFFRACTION	13	B	B	231 - 286	80 - 135
14	X-RAY DIFFRACTION	14	B	B	287 - 322	136 - 171
15	X-RAY DIFFRACTION	15	B	B	323 - 342	172 - 191
16	X-RAY DIFFRACTION	16	B	B	343 - 382	192 - 231
17	X-RAY DIFFRACTION	17	B	B	383 - 422	232 - 271
18	X-RAY DIFFRACTION	18	B	B	423 - 477	272 - 326
19	X-RAY DIFFRACTION	19	B	B	478 - 528	327 - 377
20	X-RAY DIFFRACTION	20	B	B	529 - 605	378 - 454

-
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