PDB-5is8: Crystal structure of mouse CARM1 in complex with inhibitor SA0271

ID or keywords:

Entry

Database: PDB / ID: 5is8

Title

Crystal structure of mouse CARM1 in complex with inhibitor SA0271

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

regulation of growth plate cartilage chondrocyte proliferation / endochondral bone morphogenesis / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / Cytoprotection by HMOX1 / Estrogen-dependent gene expression / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.709 Å

Authors

Cura, V. / Marechal, N. / Mailliot, J. / Troffer-Charlier, N. / Hassenboehler, P. / Wurtz, J.M. / Bonnefond, L. / Cavarelli, J.

Citation

Journal: To Be Published
Title: Crystal structure of mouse CARM1 in complex with inhibitor SA0271
Authors: Cura, V. / Marechal, N. / Mailliot, J. / Troffer-Charlier, N. / Wurtz, J.M. / Bonnefond, L. / Cavarelli, J.

History

Deposition	Mar 15, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 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	5is8.cif.gz	780.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5is8.ent.gz	667.3 KB	Display	PDB format
PDBx/mmJSON format	5is8.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/is/5is8 ftp://data.pdbj.org/pub/pdb/validation_reports/is/5is8	HTTPS FTP

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Related structure data

Related structure data	5ih3S S: Starting model for refinement
Similar structure data	5ntc-d 5u4x-d 5k8x-d 6s70-d 5tbi-d 5tbh-d 6izq-d 6s7b-d 5is6-d 5isd-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

D: Histone-arginine methyltransferase CARM1

C: Histone-arginine methyltransferase CARM1

hetero molecules

174 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)	74.544, 98.623, 207.467
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: 43109.793 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-6D1 / 5'-{[(3S)-3-amino-3-carboxypropyl](2-chloroethyl)amino}-5'-deoxyadenosine Mass: 429.859 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₆H₂₄ClN₇O₅
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.21 Å³/Da / Density % sol: 44.38 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: BTP pH 7.5 100 mM, PEG 3350 15%

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.7→18 Å / Num. obs: 39433 / % possible obs: 93.8 % / Redundancy: 3.3 % / B_iso Wilson estimate: 51.02 Å² / R_sym value: 0.102 / Net I/σ(I): 15.8
Reflection shell	Resolution: 2.7→2.75 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.4 / % possible all: 94.4

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2313: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3

Resolution: 2.709→17.994 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2424	1963	5 %	Random selection
R_work	0.1942	-	-	-
obs	0.1967	39250	92.8 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.709→17.994 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10938	0	125	71	11134

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	11368
X-RAY DIFFRACTION	f_angle_d	0.755	15424
X-RAY DIFFRACTION	f_dihedral_angle_d	15.578	6765
X-RAY DIFFRACTION	f_chiral_restr	0.047	1686
X-RAY DIFFRACTION	f_plane_restr	0.005	1975

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 (%)
2.7091-2.7766	0.3323	120	0.2586	2426	X-RAY DIFFRACTION	86
2.7766-2.8514	0.3293	146	0.2555	2638	X-RAY DIFFRACTION	94
2.8514-2.935	0.2872	125	0.2601	2688	X-RAY DIFFRACTION	94
2.935-3.0293	0.3004	142	0.2478	2627	X-RAY DIFFRACTION	93
3.0293-3.137	0.2994	154	0.2649	2631	X-RAY DIFFRACTION	93
3.137-3.2619	0.2975	131	0.2417	2648	X-RAY DIFFRACTION	93
3.2619-3.4094	0.2644	131	0.2235	2619	X-RAY DIFFRACTION	92
3.4094-3.5878	0.2542	120	0.2093	2620	X-RAY DIFFRACTION	92
3.5878-3.8106	0.2579	144	0.1893	2596	X-RAY DIFFRACTION	91
3.8106-4.1016	0.2473	153	0.1876	2617	X-RAY DIFFRACTION	92
4.1016-4.5085	0.2	143	0.1617	2686	X-RAY DIFFRACTION	94
4.5085-5.1475	0.1869	129	0.1437	2787	X-RAY DIFFRACTION	95
5.1475-6.4356	0.1947	160	0.1728	2819	X-RAY DIFFRACTION	97
6.4356-17.9945	0.2296	165	0.1685	2885	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	0.1076	-0.0755	-0.0159	0.0687	0.0191	0.0312	0.0352	-0.1117	0.2361	0.0024	-0.0046	0.0099	-0.1504	-0.0069	0.0321	0.4774	-0.1248	0.0408	0.3409	-0.0506	0.5353	55.1651	40.286	134.8564
2	0.1085	0.0019	-0.0342	0.0062	-0.0426	0.1051	0.1094	0.1086	-0.0134	0.0189	-0.0145	-0.034	-0.0296	0.0706	0.0824	0.1958	-0.021	0.0205	0.237	0.0359	0.4222	47.653	11.9196	119.4164
3	0.1471	0.0452	-0.0306	0.1765	-0.034	0.1297	0.001	0.0679	-0.0121	-0.0881	0.0149	0.0293	-0.0778	0.1794	0.0193	0.2388	-0.0972	0.0554	0.3577	-0.0261	0.391	59.8391	19.4739	119.3286
4	0.0008	0.0011	-0.003	0.0017	-0.0017	0.0014	0.032	-0.0154	-0.0515	0.0637	-0.0336	-0.0256	0.0174	-0.0068	-0	0.4119	-0.0095	-0.0646	0.6694	-0.0769	0.5767	61.3165	-4.2269	134.3079
5	0.179	0.0435	-0.0699	0.0814	0.0633	0.2118	0.2987	0.2454	0.0328	0.0945	0.0224	-0.0818	-0.2851	-0.2331	0.6841	0.1773	0.3392	0.1628	0.2614	0.1527	0.4436	18.2727	18.1689	114.92
6	0.1186	-0.0447	0.0679	0.0167	-0.0276	0.0321	0.0488	-0.0868	-0.1114	0.1391	0.0124	0.0844	-0.1225	0.1338	0.0419	0.5274	-0.1131	0.1735	0.4876	-0.0803	0.4892	38.1896	28.9889	148.9266
7	0.0441	0.0232	0.0111	0.0538	0.0488	0.0402	0.0957	-0.1471	0.081	0.0501	-0.0616	0.0205	-0.067	-0.0957	0.0067	0.4855	0.1045	0.1613	0.4518	-0.0002	0.5776	17.1602	21.3913	138.1404
8	0.3078	0.0929	0.1097	0.0458	0.0815	0.1296	0.1527	-0.0432	-0.0665	0.0903	0.0735	0.0298	-0.2377	-0.2348	0.1271	0.406	0.0792	0.1299	0.3772	0.0389	0.3538	16.9642	22.1108	140.4475
9	0.0324	-0.0083	0.0296	0.0189	0.0025	0.0204	0.1309	0.0398	-0.0295	-0.0031	0.076	-0.0355	-0.1448	-0.0422	0	0.6389	0.0869	0.1985	0.6506	0.0342	0.6333	24.7572	29.5442	141.9578
10	0.0602	0.0583	-0.0296	0.1094	-0.0081	0.0247	0.1105	0.1476	-0.0324	0.1674	0.0041	-0.0797	-0.2532	-0.0963	0.0502	1.133	0.26	0.1507	0.5948	0.0021	0.4293	21.9457	42.0472	173.8831
11	0.5434	0.1857	0.068	0.0735	0.0346	0.0393	0.1877	-0.0363	-0.2204	-0.0237	-0.0712	-0.013	-0.2728	-0.1429	0.1641	0.6677	0.1595	0.0998	0.4304	-0.0843	0.2619	25.7274	20.9497	191.1415
12	0.3245	0.428	-0.0416	0.6186	-0.0473	0.0261	0.1698	0.0992	-0.1615	0.2438	-0.2576	-0.0835	-0.1686	-0.2286	-0.0223	0.7237	0.201	0.0971	0.7296	-0.1068	0.4266	15.9763	19.844	191.3348
13	0.0009	-0.0018	-0.0021	0.003	0.0021	0.0015	0.0258	-0.0043	-0.0437	-0.038	-0.0613	0.0394	-0.0246	0.0153	-0	0.7795	0.0233	-0.0463	0.8111	0.0522	0.7422	13.2661	-2.9858	176.987
14	0.0651	-0.0182	0.0203	0.2525	-0.0683	0.0759	0.2526	-0.1328	0.0667	0.0742	-0.1197	0.2001	-0.1992	0.3697	0.0181	0.5593	-0.2154	0.0651	0.6732	-0.1195	0.408	57.2794	17.0349	196.3222
15	0.0188	-0.0195	0.0028	0.0014	-0.0019	0.0001	0.0851	0.1408	-0.1265	-0.0699	0.0086	-0.0953	-0.1292	-0.1489	0.0001	0.6959	0.0394	0.1392	0.6221	-0.0434	0.4778	39.0335	27.9535	163.6677
16	0.0241	-0.0153	-0.0058	0.0095	-0.0025	0.0157	0.0857	0.0794	-0.0836	0.0024	-0.0422	0.0936	-0.1028	0.1218	0	0.7886	-0.2484	0.1507	0.8095	-0.1087	0.5942	62.9432	23.4928	175.5459
17	0.0373	-0.0316	-0.039	0.0215	0.0329	0.0438	-0.0001	-0.0498	-0.0326	-0.0957	0.0473	0.056	-0.0207	0.2264	-0	0.5476	-0.0309	0.0442	0.6253	-0.0893	0.4288	57.9103	17.5327	170.2383
18	0.0261	-0.0142	0.027	0.0155	-0.0007	0.0287	0.026	0.076	0.0258	0.0418	0.0273	0.0749	0.0056	-0.087	0	0.767	-0.0436	0.1971	0.7394	-0.0676	0.5488	53.7072	29.6624	168.9955

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 136:282)
2	X-RAY DIFFRACTION	2	(chain A and resid 283:349)
3	X-RAY DIFFRACTION	3	(chain A and resid 350:478)
4	X-RAY DIFFRACTION	4	(chain A and resid 479:497)
5	X-RAY DIFFRACTION	5	(chain B and resid 136:293)
6	X-RAY DIFFRACTION	6	(chain B and resid 294:336)
7	X-RAY DIFFRACTION	7	(chain B and resid 337:365)
8	X-RAY DIFFRACTION	8	(chain B and resid 366:445)
9	X-RAY DIFFRACTION	9	(chain B and resid 446:478)
10	X-RAY DIFFRACTION	10	(chain C and resid 136:257)
11	X-RAY DIFFRACTION	11	(chain C and resid 258:336)
12	X-RAY DIFFRACTION	12	(chain C and resid 337:478)
13	X-RAY DIFFRACTION	13	(chain C and resid 479:497)
14	X-RAY DIFFRACTION	14	(chain D and resid 136:293)
15	X-RAY DIFFRACTION	15	(chain D and resid 294:344)
16	X-RAY DIFFRACTION	16	(chain D and resid 345:372)
17	X-RAY DIFFRACTION	17	(chain D and resid 373:430)
18	X-RAY DIFFRACTION	18	(chain D and resid 431:478)

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