PDB-5isf: Crystal structure of mouse CARM1 in complex with inhibitor SA0705

ID or keywords:

Entry

Database: PDB / ID: 5isf

Title

Crystal structure of mouse CARM1 in complex with inhibitor SA0705

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: 2.22 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 SA0705
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	5isf.cif.gz	801.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5isf.ent.gz	683.5 KB	Display	PDB format
PDBx/mmJSON format	5isf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5isf_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	5isf_full_validation.pdf.gz	1.7 MB	Display
Data in XML	5isf_validation.xml.gz	53.7 KB	Display
Data in CIF	5isf_validation.cif.gz	72.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/is/5isf ftp://data.pdbj.org/pub/pdb/validation_reports/is/5isf	HTTPS FTP

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Related structure data

Related structure data	5ih3S S: Starting model for refinement
Similar structure data	6s7b-d 5u4x-d 5tbi-d 6s71-d 5ih3-d 4ikp-d 5tbh-d 5lv3-d 5isc-d 5is6-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

167 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)	74.742, 98.137, 206.674
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 , 8 types, 405 molecules

#2: Chemical	ChemComp-6D4 / 5'-{[(3S)-3-amino-3-carboxypropyl][2-(triazan-1-yl)ethyl]amino}-5'-deoxyadenosine Mass: 440.458 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₆H₂₈N₁₀O₅
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Chemical	ChemComp-M2M / 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE Mass: 134.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₃
#7: Chemical	ChemComp-DXE / 1,2-DIMETHOXYETHANE Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#8: 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.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₁N₆O₅S
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.32 Å³/Da / Density % sol: 46.97 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris-HCl pH 8.0 100 mM PEG 2000 MME 10 % NaCl 167 mM

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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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.2→20 Å / Num. obs: 73738 / % possible obs: 98.7 % / Redundancy: 4.4 % / B_iso Wilson estimate: 42.88 Å² / R_sym value: 0.092 / Net I/σ(I): 16.7
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.5 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	dev_1980	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3

Resolution: 2.22→20 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.38

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2013	3645	4.95 %	Random selection
R_work	0.1656	-	-	-
obs	0.1674	73679	97.14 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.22→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11004	0	235	384	11623

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	11585
X-RAY DIFFRACTION	f_angle_d	0.736	15664
X-RAY DIFFRACTION	f_dihedral_angle_d	13.704	4182
X-RAY DIFFRACTION	f_chiral_restr	0.036	1707
X-RAY DIFFRACTION	f_plane_restr	0.002	1999

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 (%)
2.2199-2.2491	0.2436	79	0.2054	1579	X-RAY DIFFRACTION	57
2.2491-2.2799	0.2259	145	0.207	2656	X-RAY DIFFRACTION	98
2.2799-2.3124	0.2541	127	0.1989	2696	X-RAY DIFFRACTION	98
2.3124-2.3469	0.253	124	0.2014	2717	X-RAY DIFFRACTION	99
2.3469-2.3835	0.2265	126	0.1954	2747	X-RAY DIFFRACTION	99
2.3835-2.4225	0.2489	164	0.2031	2671	X-RAY DIFFRACTION	99
2.4225-2.4642	0.2207	143	0.1925	2706	X-RAY DIFFRACTION	99
2.4642-2.5089	0.2582	128	0.1878	2717	X-RAY DIFFRACTION	99
2.5089-2.5571	0.2501	151	0.1934	2705	X-RAY DIFFRACTION	99
2.5571-2.6092	0.2448	135	0.1961	2684	X-RAY DIFFRACTION	99
2.6092-2.6658	0.2281	147	0.1953	2739	X-RAY DIFFRACTION	99
2.6658-2.7277	0.2419	135	0.1864	2722	X-RAY DIFFRACTION	99
2.7277-2.7957	0.2383	142	0.1905	2706	X-RAY DIFFRACTION	98
2.7957-2.8711	0.2402	141	0.1972	2720	X-RAY DIFFRACTION	98
2.8711-2.9553	0.2377	126	0.2001	2719	X-RAY DIFFRACTION	99
2.9553-3.0504	0.2197	156	0.2011	2730	X-RAY DIFFRACTION	99
3.0504-3.159	0.2291	150	0.1979	2733	X-RAY DIFFRACTION	99
3.159-3.285	0.2249	139	0.1899	2750	X-RAY DIFFRACTION	99
3.285-3.4338	0.2143	134	0.176	2768	X-RAY DIFFRACTION	99
3.4338-3.6139	0.1944	126	0.1664	2750	X-RAY DIFFRACTION	99
3.6139-3.8389	0.183	157	0.1508	2731	X-RAY DIFFRACTION	99
3.8389-4.1329	0.1808	162	0.1374	2783	X-RAY DIFFRACTION	99
4.1329-4.5445	0.1522	148	0.1234	2764	X-RAY DIFFRACTION	99
4.5445-5.1923	0.1651	130	0.12	2810	X-RAY DIFFRACTION	99
5.1923-6.5053	0.1834	160	0.1594	2829	X-RAY DIFFRACTION	99
6.5053-20.1879	0.1872	170	0.1626	2902	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	0.6104	-0.4666	-0.1346	0.6952	0.0665	0.6685	0.0504	-0.0807	0.1115	0.0852	-0.0475	0.078	-0.1148	-0.0103	0	0.3706	-0.0804	0.0363	0.3453	-0.0715	0.3338	55.0773	40.2205	133.0741
2	0.8201	0.1937	0.301	-0.274	0.0652	0.3349	0.0707	-0.0109	0.0273	-0.0076	-0.0513	0.0633	0.0336	0.0432	-0	0.2546	-0.0218	0.0097	0.2698	-0.0144	0.3829	47.6661	11.8587	118.8904
3	0.922	0.1684	-0.1869	1.1312	-0.0396	1.2628	-0.0238	-0.0397	-0.0443	-0.0385	-0.0128	-0.0983	0.0749	0.0179	-0	0.2441	-0.0488	0.0467	0.3021	-0.0212	0.3148	60.3116	19.1472	119.0121
4	0.8031	-0.4234	-0.4752	0.6111	0.2687	1.5821	0.1323	0.0776	0.029	-0.0007	0.0351	-0.0674	-0.1908	-0.119	0	0.2809	0.0384	0.0341	0.2661	0.0373	0.3476	18.8381	19.7152	115.0054
5	0.3894	0.2539	0.1349	-0.2458	-0.1396	0.0037	0.2	-0.0778	-0.311	0.1956	-0.0049	-0.0283	-0.0301	0.0387	0	0.4524	-0.0794	0.0803	0.5056	-0.0401	0.4363	38.3592	29.274	148.2216
6	0.1094	-0.1141	-0.1581	0.5032	0.6323	0.6789	0.1018	-0.0976	0.0704	0.064	-0.0676	-0.0082	0.0604	-0.2029	-0	0.3609	0.0011	0.067	0.4295	0.0368	0.4595	17.1416	21.9114	137.7075
7	0.6149	0.0684	-0.1365	-0.2006	0.3612	0.9752	0.1339	-0.1177	-0.0706	0.0133	0.0108	-0.049	-0.1255	-0.0194	0	0.3753	-0.0037	0.0419	0.3983	0.0367	0.3528	17.0149	22.613	140.0579
8	0.5623	0.1587	0.666	0.4342	0.2204	0.5513	0.0915	-0.1863	0.0687	0.0524	-0.0919	-0.2624	-0.178	0.0975	0	0.3945	-0	0.1016	0.4314	-0.0133	0.4489	24.916	29.7106	141.4542
9	0.9667	0.5248	-0.5571	0.4811	-0.2899	1.0841	0.0047	0.0822	0.1599	0.0851	0.0484	0.026	-0.1278	0.0362	0	0.5955	0.0706	0.0249	0.5525	0.0319	0.4909	23.0648	42.268	175.1614
10	0.2146	-0.0742	0.148	0.2571	-0.2328	0.3754	0.01	0.0044	-0.0943	0.1193	0.0276	0.1302	-0.0807	-0.0589	0	0.4397	0.0335	0.0191	0.3924	0.0011	0.4328	26.1044	20.8529	190.5235
11	0.5118	0.084	-0.5221	0.6387	0.0779	0.4405	-0.0272	0.085	-0.1429	0.0853	-0.0573	0.1658	-0.0324	-0.0181	-0	0.4904	0.0596	0.0585	0.4794	-0.0105	0.4599	16.2268	20.2073	190.5146
12	0.9814	0.4612	-0.4343	0.7297	-0.389	0.79	0.1281	-0.1137	-0.0432	0.0335	-0.0834	-0.0552	-0.1019	0.1015	0	0.5063	-0.0176	0.004	0.4345	-0.0148	0.4247	57.1698	18.0832	195.3036
13	0.2665	-0.5498	0.2866	-0.0516	0.0671	0.061	0.239	0.3724	-0.2439	-0.1699	-0.1275	0.1375	0.0115	0.0206	0	0.512	0.0282	0.0762	0.5812	-0.0278	0.4948	39.7214	28.258	163.4703
14	0.3293	-0.1299	-0.1366	0.1586	-0.166	0.3459	-0.1747	0.0898	-0.1459	0.0166	-0.0246	0.1258	-0.0718	0.5287	-0.0001	0.4987	-0.0003	0.0415	0.551	-0.0177	0.4552	63.6242	23.4056	174.9814
15	0.1712	0.2319	-0.3397	0.1094	-0.211	0.3288	-0.0194	0.0176	-0.1288	0.0013	-0.0848	-0.0222	0.1177	0.0312	-0	0.5529	0.0301	0.0519	0.4866	-0.0465	0.4294	58.3834	17.6591	169.6154
16	0.2986	-0.0049	0.3521	0.1886	0.0325	0.3017	0.0175	0.136	-0.1401	0.0709	-0.1642	0.1598	-0.195	0.0124	-0	0.551	0.0663	0.0753	0.5488	-0.0574	0.4808	53.851	29.1427	168.772

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 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 446:478)
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 431:478)

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