PDB-5isc: Crystal structure of mouse CARM1 in complex with inhibitor SA0491

ID or keywords:

Entry

Database: PDB / ID: 5isc

Title

Crystal structure of mouse CARM1 in complex with inhibitor SA0491

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 / type I protein arginine methyltransferase / negative regulation of dendrite development / protein-arginine omega-N asymmetric methyltransferase activity ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 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 SA0491
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	5isc.cif.gz	791.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5isc.ent.gz	677 KB	Display	PDB format
PDBx/mmJSON format	5isc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5isc_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	5isc_full_validation.pdf.gz	1.5 MB	Display
Data in XML	5isc_validation.xml.gz	49.1 KB	Display
Data in CIF	5isc_validation.cif.gz	66.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/is/5isc ftp://data.pdbj.org/pub/pdb/validation_reports/is/5isc	HTTPS FTP

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Related structure data

Related structure data	5ih3S S: Starting model for refinement
Similar structure data	5tbi-d 5isa-d 5lv2-1 5lv3-d 5ish-d 5is7-d 6s7a-d 6s79-d 5tbj-d 5k8x-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

166 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	79.123, 101.043, 211.349
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

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Protein , 1 types, 4 molecules ABCD

#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

#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

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Non-polymers , 6 types, 133 molecules

#2: Chemical	ChemComp-SAO / 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 385.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₁N₆O₅S
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-6D0 / 5'-{[(3S)-3-amino-3-carboxypropyl](3-bromo-2-oxopropyl)amino}-5'-deoxyadenosine Mass: 502.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₄BrN₇O₆
#5: Chemical	ChemComp-DXE / 1,2-DIMETHOXYETHANE Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#6: Chemical	ChemComp-M2M / 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.59 Å³/Da / Density % sol: 52.42 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris-HCl pH 8.0 100 mM PEG 2000 MME 19 %

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.6→20 Å / Num. obs: 47376 / % possible obs: 88.1 % / Redundancy: 5.5 % / B_iso Wilson estimate: 50.89 Å² / R_sym value: 0.095 / Net I/σ(I): 19.9
Reflection shell	Resolution: 2.6→2.69 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.8 / % possible all: 78.7

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Processing

Software

Name	Version	Classification
PHENIX	dev_1951	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3

Resolution: 2.6→20 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.51

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2389	2373	5.02 %	Random Selection
R_work	0.2056	-	-	-
obs	0.2073	47290	87.63 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10991	0	159	120	11270

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11439
X-RAY DIFFRACTION	f_angle_d	1.178	15490
X-RAY DIFFRACTION	f_dihedral_angle_d	14.074	4149
X-RAY DIFFRACTION	f_chiral_restr	0.049	1694
X-RAY DIFFRACTION	f_plane_restr	0.005	1995

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 (%)
2.5821-2.6347	0.3408	113	0.2976	2080	X-RAY DIFFRACTION	70
2.6347-2.6918	0.3074	122	0.2767	2405	X-RAY DIFFRACTION	81
2.6918-2.7543	0.3118	123	0.2674	2398	X-RAY DIFFRACTION	80
2.7543-2.823	0.2845	125	0.2615	2398	X-RAY DIFFRACTION	80
2.823-2.8991	0.2809	126	0.2743	2368	X-RAY DIFFRACTION	80
2.8991-2.9841	0.2928	122	0.267	2376	X-RAY DIFFRACTION	79
2.9841-3.0801	0.2801	121	0.27	2361	X-RAY DIFFRACTION	79
3.0801-3.1897	0.2684	127	0.2538	2386	X-RAY DIFFRACTION	80
3.1897-3.3169	0.275	135	0.2469	2417	X-RAY DIFFRACTION	81
3.3169-3.4671	0.2823	141	0.2306	2588	X-RAY DIFFRACTION	86
3.4671-3.6488	0.251	129	0.219	2848	X-RAY DIFFRACTION	94
3.6488-3.8758	0.2255	147	0.2009	2980	X-RAY DIFFRACTION	99
3.8758-4.1725	0.2483	178	0.1832	3007	X-RAY DIFFRACTION	100
4.1725-4.5878	0.1761	174	0.1596	3007	X-RAY DIFFRACTION	100
4.5878-5.241	0.1763	136	0.1461	3058	X-RAY DIFFRACTION	100
5.241-6.5633	0.2186	169	0.1941	3081	X-RAY DIFFRACTION	100
6.5633-19.8706	0.2422	185	0.2011	3159	X-RAY DIFFRACTION	98

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	2.7589	-0.6819	-1.2092	2.2155	0.8496	2.5258	0.0886	-0.0858	0.2594	-0.027	0.0187	-0.0291	-0.4255	-0.0217	-0.1345	0.71	-0.1533	0.0388	0.4779	-0.0013	0.407	55.6824	42.6908	135.9492
2	3.046	1.513	0.9549	1.2462	0.4144	1.4873	0.2518	-0.2194	-0.1725	0.1078	-0.1776	-0.2338	-0.025	0.2627	-0.0201	0.2822	-0.0503	0.0508	0.3153	0.0202	0.3823	49.648	12.9923	121.5407
3	0.9891	0.5499	-0.5621	3.2057	0.5664	1.9256	0.0241	-0.0392	-0.165	-0.0958	-0.1079	-0.3204	-0.0903	0.2852	0.0267	0.3923	-0.1483	0.062	0.5038	0.04	0.4421	62.4917	21.4451	121.6626
4	2.0707	-0.839	-0.2388	2.4275	0.7783	3.2986	0.1671	0.0999	0.1004	-0.0206	-0.1102	0.0255	-0.3681	-0.3083	-0.0511	0.405	0.078	0.0324	0.3549	0.0366	0.3569	18.5909	18.6671	117.2703
5	6.6401	3.7915	-1.0634	2.0169	-0.6045	0.1671	0.3613	-0.7484	-0.5821	0.2741	-0.3379	-0.2671	-0.3786	0.0862	-0.0687	0.6131	-0.0866	0.0143	0.5543	0.0651	0.4084	38.6872	30.4292	151.4124
6	2.7842	0.0062	0.2814	1.5458	0.3781	3.6932	-0.0236	-0.4109	-0.0113	0.0416	0.0107	0.0321	0.0071	-0.4423	-0.0251	0.3882	0.0468	0.1313	0.4463	-0.0005	0.4337	16.8809	21.1727	140.6849
7	1.8148	-0.6649	0.9494	1.4233	1.5123	3.6387	0.0235	-0.2568	-0.0212	0.0874	-0.0144	0.0231	-0.2366	-0.3176	0.022	0.3585	0.019	0.0969	0.4776	0.0843	0.311	16.7371	21.9261	143.0631
8	1.0171	-0.3907	1.3192	2.0157	-0.0524	1.6966	-0.0187	0.1003	0.0164	-0.675	-0.1118	-0.4363	-0.1824	0.2149	0.0454	0.5647	-0.0299	0.1505	0.5317	0.0405	0.5145	24.0156	30.1428	144.5496
9	4.446	1.5896	-0.2179	3.0308	0.5753	2.3383	0.0802	0.0515	0.4208	-0.2013	0.0004	-0.1466	-0.2404	-0.0566	-0.0667	0.573	0.1082	0.0546	0.3696	0.0975	0.405	21.6967	42.2593	178.9478
10	0.683	0.0536	0.6662	0.2706	-0.227	1.0946	0.2799	0.1662	-0.1304	-0.2594	-0.1715	0.2059	-0.0315	-0.0967	-0.0982	0.2466	0.073	0.0735	0.2891	0.0245	0.3317	26.29	20.8316	194.6949
11	0.8965	-0.4759	-0.4664	3.689	-0.4063	2.5268	-0.027	-0.0234	-0.0819	0.0967	0.0358	0.0398	0.1124	-0.0453	-0.0245	0.1936	0.106	0.0631	0.4097	0.0289	0.3776	15.9213	19.068	194.8532
12	1.7469	0.674	-1.268	2.4399	-0.8365	3.5522	0.291	-0.1877	0.2469	-0.0164	-0.0134	0.0277	-0.6022	0.3278	-0.2276	0.3519	-0.1101	0.0756	0.347	-0.0707	0.4237	59.1047	20.1496	199.6519
13	6.5133	-4.1495	-0.2044	1.5788	0.6256	0.5341	0.4844	0.4365	-0.2818	-0.5478	-0.2463	0.0566	-0.0656	0.006	-0.1491	0.5895	0.0176	0.1479	0.4207	0.0124	0.484	40.0067	29.0289	166.7279
14	1.543	-0.9788	0.7768	2.107	-1.5795	4.3439	0.2249	0.1144	-0.0547	-0.0721	-0.2107	0.0259	-0.5434	0.5848	-0.1923	0.3299	-0.111	0.1139	0.4871	-0.0481	0.5199	65.4227	25.9452	178.5994
15	2.2177	-0.5731	0.856	1.8422	-1.66	3.5477	0.0021	0.3488	-0.0883	-0.3118	-0.081	-0.1617	-0.116	0.0888	0.0409	0.3402	-0.0105	0.0864	0.354	-0.0846	0.3175	60.6114	19.6554	173.2025
16	3.3049	0.8273	0.4546	2.5221	0.5685	6.4672	0.1585	-0.1189	-0.09	0.2524	-0.2012	0.2989	-0.78	0.3461	0.11	0.4756	-0.0047	0.0865	0.42	0.0116	0.4716	55.3289	31.4926	171.9786

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 137:282)
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 B and resid 136:293)
5	X-RAY DIFFRACTION	5	(chain B and resid 294:336)
6	X-RAY DIFFRACTION	6	(chain B and resid 337:365)
7	X-RAY DIFFRACTION	7	(chain B and resid 366:445)
8	X-RAY DIFFRACTION	8	(chain B and resid 446:477)
9	X-RAY DIFFRACTION	9	(chain C and resid 136:257)
10	X-RAY DIFFRACTION	10	(chain C and resid 258:336)
11	X-RAY DIFFRACTION	11	(chain C and resid 337:478)
12	X-RAY DIFFRACTION	12	(chain D and resid 136:293)
13	X-RAY DIFFRACTION	13	(chain D and resid 294:344)
14	X-RAY DIFFRACTION	14	(chain D and resid 345:372)
15	X-RAY DIFFRACTION	15	(chain D and resid 373:430)
16	X-RAY DIFFRACTION	16	(chain D and resid 431:477)

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