PDB-5lv3: Crystal structure of mouse CARM1 in complex with ligand LH1561Br

ID or keywords:

Entry

Database: PDB / ID: 5lv3

Title

Crystal structure of mouse CARM1 in complex with ligand LH1561Br

Components

Histone-arginine methyltransferase CARM1

Keywords

TRANSFERASE / PROTEIN ARGININE METHYLTRANSFERASE /

CATALYTIC DOMAIN / CHROMATIN REGULATOR /

MRNA PROCESSING /

MRNA SPLICING /

NUCLEUS /

S-ADENOSYL-L-METHIONINE /

TRANSCRIPTION /

TRANSCRIPTION REGULATION

Function / homology

Function and homology information

histone H3R26 methyltransferase activity / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / negative regulation of dendrite development / type I protein arginine methyltransferase / Cytoprotection by HMOX1 ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Cura, V. / Marechal, N. / Troffer-Charlier, N. / Halby, L. / Arimondo, P. / Bonnefond, L. / Cavarelli, J.

Citation

Journal: Philos. Trans. R. Soc. Lond., B, Biol. Sci. / Year: 2018
Title: Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors.
Authors: Halby, L. / Marechal, N. / Pechalrieu, D. / Cura, V. / Franchini, D.M. / Faux, C. / Alby, F. / Troffer-Charlier, N. / Kudithipudi, S. / Jeltsch, A. / Aouadi, W. / Decroly, E. / Guillemot, J. ...

History

Deposition	Sep 12, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 2, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5lv3.cif.gz	806.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5lv3.ent.gz	685.1 KB	Display	PDB format
PDBx/mmJSON format	5lv3.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/lv/5lv3 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/5lv3	HTTPS FTP

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Related structure data

Related structure data	5lv2C 5lv4C 5lv5C 5tbhC 5tbiC 5tbjC 5ih3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5lv2-1 5is6-d 6s77-d 6s7a-d 6s71-d 5tbi-d 2y1w-d 6s79-d 5dwq-d 5k8v-d 5lv2-2 6s7c-d 2y1x-d 5is7-d 5tbj-d 5k8x-d 6arj-d 5isg-d 5tbh-d 5u4x-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (3) #155 - Nov 2012 Vitamin D Receptor similarity (2) #63 - Mar 2005 T-Cell Receptor similarity (1)

Deposited unit

A: Histone-arginine methyltransferase CARM1

B: Histone-arginine methyltransferase CARM1

C: Histone-arginine methyltransferase CARM1

D: Histone-arginine methyltransferase CARM1

hetero molecules

165 kDa, 4 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)	75.092, 98.524, 208.097
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Histone-arginine methyltransferase CARM1 / Coactivator-associated arginine methyltransferase 1 / Protein arginine N-methyltransferase 4 Mass: 40850.457 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Carm1, Prmt4 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9WVG6, type I protein arginine methyltransferase
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-LHF / 5-[[2-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethylamino]methyl]-4-azanyl-1-[2-(4-bromanylphenoxy)ethyl]pyrimidin-2-one Mass: 602.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₄H₂₈BrN₉O₅
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1126 / 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: 2.36 Å³/Da / Density % sol: 47.78 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris-HCl pH 8.0 100 mM PEG 2000 MME 15% NaCl 100 mM

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 11, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. obs: 143500 / % possible obs: 100 % / Redundancy: 7.9 % / B_iso Wilson estimate: 21.8 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.156 / Net I/σ(I): 8.7
Reflection shell	Resolution: 1.8→1.82 Å / Redundancy: 7.9 % / R_merge(I) obs: 1.867 / Mean I/σ(I) obs: 1.1 / CC_1/2: 0.302 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2386: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3

Resolution: 1.8→29.992 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 19.89

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.203	7112	4.96 %	Random selection
R_work	0.1735	-	-	-
obs	0.175	143435	99.97 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 30.85 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.992 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10985	0	130	1126	12241

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	11405
X-RAY DIFFRACTION	f_angle_d	0.814	15460
X-RAY DIFFRACTION	f_dihedral_angle_d	13.85	6754
X-RAY DIFFRACTION	f_chiral_restr	0.049	1687
X-RAY DIFFRACTION	f_plane_restr	0.004	2027

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 (%)
1.8-1.8205	0.3406	255	0.3153	4498	X-RAY DIFFRACTION	100
1.8205-1.8419	0.2848	212	0.287	4476	X-RAY DIFFRACTION	100
1.8419-1.8643	0.2839	219	0.2887	4519	X-RAY DIFFRACTION	100
1.8643-1.8879	0.3366	221	0.2801	4526	X-RAY DIFFRACTION	100
1.8879-1.9128	0.2832	268	0.2614	4451	X-RAY DIFFRACTION	100
1.9128-1.939	0.2939	233	0.2462	4512	X-RAY DIFFRACTION	100
1.939-1.9667	0.272	214	0.2346	4527	X-RAY DIFFRACTION	100
1.9667-1.996	0.2296	238	0.2269	4476	X-RAY DIFFRACTION	100
1.996-2.0272	0.2639	246	0.2172	4507	X-RAY DIFFRACTION	100
2.0272-2.0604	0.2361	251	0.2051	4465	X-RAY DIFFRACTION	100
2.0604-2.0959	0.2246	225	0.1991	4523	X-RAY DIFFRACTION	100
2.0959-2.134	0.2378	219	0.1862	4538	X-RAY DIFFRACTION	100
2.134-2.1751	0.2279	246	0.1856	4496	X-RAY DIFFRACTION	100
2.1751-2.2195	0.2355	247	0.1779	4501	X-RAY DIFFRACTION	100
2.2195-2.2677	0.2148	248	0.1707	4498	X-RAY DIFFRACTION	100
2.2677-2.3204	0.2009	214	0.1708	4523	X-RAY DIFFRACTION	100
2.3204-2.3784	0.2139	222	0.1668	4561	X-RAY DIFFRACTION	100
2.3784-2.4427	0.1866	251	0.1723	4510	X-RAY DIFFRACTION	100
2.4427-2.5146	0.2008	228	0.1642	4562	X-RAY DIFFRACTION	100
2.5146-2.5957	0.2046	241	0.1649	4527	X-RAY DIFFRACTION	100
2.5957-2.6884	0.1823	242	0.1578	4527	X-RAY DIFFRACTION	100
2.6884-2.796	0.1955	225	0.1548	4551	X-RAY DIFFRACTION	100
2.796-2.9231	0.1934	229	0.1587	4555	X-RAY DIFFRACTION	100
2.9231-3.0771	0.1787	236	0.1645	4577	X-RAY DIFFRACTION	100
3.0771-3.2696	0.1987	242	0.1619	4582	X-RAY DIFFRACTION	100
3.2696-3.5217	0.1883	228	0.1574	4589	X-RAY DIFFRACTION	100
3.5217-3.8755	0.1726	246	0.1466	4593	X-RAY DIFFRACTION	100
3.8755-4.4347	0.1498	260	0.1319	4627	X-RAY DIFFRACTION	100
4.4347-5.5814	0.1646	227	0.1338	4683	X-RAY DIFFRACTION	100
5.5814-29.9964	0.2061	279	0.1929	4843	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	0.7283	-0.2703	0.1771	0.762	0.0532	1.2878	0.0074	-0.1221	0.1161	0.1442	-0.0627	0.0793	-0.0867	-0.0431	0.0662	0.17	-0.0613	0.0309	0.1575	-0.0617	0.137	55.1489	40.1504	134.1754
2	0.5881	0.1905	0.3732	0.0418	0.1359	0.3064	0.0842	-0.059	-0.0809	0.0081	-0.0389	-0.0335	-0.0162	0.0443	-0.0485	0.0897	-0.0196	0.0078	0.1038	-0.0107	0.1639	47.4517	13.8606	118.9094
3	0.4339	0.2897	-0.0589	1.4578	0.0709	0.8339	0.0053	-0.0259	-0.0757	-0.0062	-0.0077	-0.0722	0.0344	0.0375	0.0085	0.0886	-0.0291	0.0269	0.1199	-0.0157	0.1172	60.145	18.658	120.3497
4	3.8122	-1.1619	0.2179	3.8187	0.7969	1.4797	0.1206	0.0721	0.3042	-0.2368	0.1802	-0.2792	-0.4325	0.2186	-0.1418	0.2601	-0.0204	0.1086	0.1718	-0.0187	0.2235	28.568	32.8613	118.9499
5	1.4969	-0.4487	0.0636	0.1573	0.0338	1.0015	0.189	-0.0282	-0.0362	0.0867	0.0165	-0.0847	0.0306	0.0699	-0.1421	0.1408	0.0156	0.0033	0.1114	-0.0249	0.1631	23.1104	10.2549	121.7356
6	1.0945	0.2941	-0.7092	1.6407	-0.2632	0.9241	0.0963	0.1105	-0.0783	-0.0216	-0.0213	-0.0168	-0.0162	-0.1767	-0.0399	0.1129	0.0316	0.0089	0.1527	0.0289	0.1533	14.3871	14.6421	111.1303
7	0.8779	-0.6464	0.0141	0.7596	0.1469	0.8884	0.1745	0.2081	0.076	-0.1715	-0.0657	-0.0217	-0.1172	-0.1246	-0.1057	0.1375	0.0329	0.0157	0.1235	0.0318	0.1483	21.0713	19.3963	106.4212
8	0.472	0.0767	-0.4218	0.4944	-0.1647	1.0189	0.139	0.0075	0.1068	0.0463	-0.0414	0.0288	-0.1856	-0.1349	-0.1259	0.1414	0.0333	0.0335	0.1338	0.0345	0.156	14.9824	23.7008	125.7344
9	1.7179	0.8896	0.206	0.48	0.074	0.0437	0.1544	-0.2187	-0.1723	0.2946	-0.1149	0.0178	-0.0064	-0.1117	-0.0418	0.2956	-0.0704	0.074	0.3419	-0.0312	0.2029	42.0538	30.8063	149.5829
10	1.3165	-0.1387	0.3421	0.8779	0.2625	1.4771	0.1531	-0.132	0.1058	0.05	-0.0624	0.0463	0.0324	-0.0629	-0.0583	0.1662	-0.0179	0.0587	0.1829	0.0131	0.1675	16.9796	23.3969	137.2966
11	0.8943	0.0271	0.1496	0.3022	0.3982	1.2059	0.1499	-0.2769	-0.008	0.161	-0.0178	-0.0489	0.064	-0.0296	-0.1105	0.2034	-0.0323	0.0254	0.2017	0.033	0.1515	17.3047	20.0233	141.8414
12	0.736	0.2097	0.3608	0.7144	-0.2546	0.9871	0.154	-0.2371	0.1952	-0.0087	-0.027	-0.1063	-0.1182	0.1218	-0.0949	0.2015	-0.0199	0.0541	0.2378	-0.0233	0.1817	23.102	31.1392	141.9416
13	1.3393	0.2478	-0.4427	0.721	-0.1814	1.2981	-0.0402	0.1007	0.1128	-0.0382	0.0339	0.0388	-0.12	-0.0092	0.0084	0.2428	0.0523	0.0053	0.2199	0.0184	0.1423	22.6833	41.5175	178.1743
14	0.8476	-0.1468	0.372	0.4662	-0.2209	0.4784	0.1075	0.0321	-0.1801	0.0209	-0.0522	0.1867	0.0066	-0.0182	-0.0463	0.1698	0.0061	0.015	0.1386	-0.0078	0.155	28.7389	14.6919	193.6329
15	1.0166	-0.4274	0.0368	1.2712	-0.4363	0.4954	-0.0005	0.067	-0.2592	0.0228	0.0133	0.3166	0.0094	-0.0904	-0.0135	0.2296	0.0333	0.0331	0.2546	-0.0121	0.2724	13.6826	20.655	188.9878
16	1.1783	0.3315	0.2923	1.446	0.1528	0.5959	-0.0824	-0.0159	-0.1351	0.2154	-0.0221	0.246	0.0631	0.028	0.1269	0.2851	0.0345	0.091	0.2339	0.0008	0.2382	21.4327	19.9757	197.9869
17	1.1614	0.4155	-0.2557	1.3714	-0.4867	1.1341	0.0658	-0.131	-0.0221	0.1067	-0.0391	-0.1509	-0.065	0.0105	-0.0359	0.1737	-0.011	-0.0064	0.164	-0.0142	0.1335	55.5587	16.6849	198.8374
18	0.2612	0.0527	-0.0154	0.1992	-0.0548	0.9882	0.0546	0.0629	-0.0209	-0.0408	-0.0682	-0.0719	-0.128	0.0018	-0.0038	0.2369	0.0222	0.0163	0.1977	-0.0182	0.1856	61.7618	21.8281	186.5798
19	1.4593	-0.9363	0.2895	0.64	-0.1443	0.0876	0.199	0.3861	-0.1779	-0.3717	-0.1304	-0.0716	-0.0828	0.1042	-0.0019	0.3574	0.0497	0.0751	0.4371	-0.0046	0.2225	35.3348	31.4617	162.846
20	0.6989	-0.0527	0.3773	0.4676	-0.7763	1.2963	0.0609	0.2644	-0.1015	-0.1225	-0.072	0.0183	0.1154	0.0891	0.0205	0.2856	0.0526	0.0467	0.2842	-0.0393	0.189	59.1963	19.5784	171.8621
21	0.3664	-0.1149	0.4326	0.5583	0.2429	0.7697	-0.0429	0.2389	-0.0506	0.1192	-0.0528	0.0523	-0.0038	-0.1023	0.0668	0.3108	0.0489	0.0569	0.3537	-0.0073	0.1891	54.5352	30.5572	170.2156

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 136 through 279 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 280 through 336 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 337 through 478 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 135 through 155 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 156 through 179 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 180 through 217 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 218 through 253 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 254 through 300 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 301 through 336 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 337 through 369 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 370 through 433 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 434 through 477 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 136 through 279 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 280 through 337 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 338 through 433 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 434 through 477 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 136 through 253 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 254 through 300 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 301 through 336 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 337 through 433 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 434 through 476 )

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