PDB-5ise: Crystal structure of mouse CARM1 in complex with inhibitor SA0649

ID or keywords:

Entry

Database: PDB / ID: 5ise

Title

Crystal structure of mouse CARM1 in complex with inhibitor SA0649

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 / histone H3R26 methyltransferase activity / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 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 SAH at 1.8 Angstroms resolution
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	Mar 25, 2020	Group: Derived calculations Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2	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	5ise.cif.gz	814.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5ise.ent.gz	694 KB	Display	PDB format
PDBx/mmJSON format	5ise.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ise_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	5ise_full_validation.pdf.gz	1.8 MB	Display
Data in XML	5ise_validation.xml.gz	59.5 KB	Display
Data in CIF	5ise_validation.cif.gz	84.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/is/5ise ftp://data.pdbj.org/pub/pdb/validation_reports/is/5ise	HTTPS FTP

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Related structure data

Related structure data	5ih3SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3avt-d 3avv-d 3avw-d 3vnv-d 3vnu-d 3agp-d 5nxb-d 2rc5-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

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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

A: Histone-arginine methyltransferase CARM1

B: Histone-arginine methyltransferase CARM1

hetero molecules

A: Histone-arginine methyltransferase CARM1

B: Histone-arginine methyltransferase CARM1

hetero molecules

defined by author&software
167 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Histone-arginine methyltransferase CARM1

D: Histone-arginine methyltransferase CARM1

hetero molecules

C: Histone-arginine methyltransferase CARM1

D: Histone-arginine methyltransferase CARM1

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.740, 98.296, 206.234
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 , 7 types, 789 molecules

#2: Chemical	ChemComp-6D2 / 5'-{[(3S)-3-amino-3-carboxypropyl](3-carbamimidamidopropyl)amino}-5'-deoxyadenosine Mass: 466.495 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₈H₃₀N₁₀O₅
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-DXE / 1,2-DIMETHOXYETHANE Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Chemical	ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₉
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 771 / 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: 46.94 %
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 133 mM

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9801 Å / Relative weight: 1
Reflection	Resolution: 2.1→30 Å / Num. obs: 87823 / % possible obs: 97.9 % / Redundancy: 6.2 % / B_iso Wilson estimate: 27.66 Å² / R_sym value: 0.077 / Net I/σ(I): 24.4
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4.9 / % possible all: 91.6

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Processing

Software

Name	Version	Classification
PHENIX	dev_1839	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3

Resolution: 2.1→30 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.68

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2002	4347	4.95 %	Random selection
R_work	0.1509	-	-	-
obs	0.1534	87753	97.84 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10985	0	235	771	11991

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	11587
X-RAY DIFFRACTION	f_angle_d	1.41	15673
X-RAY DIFFRACTION	f_dihedral_angle_d	19.624	4301
X-RAY DIFFRACTION	f_chiral_restr	0.058	1702
X-RAY DIFFRACTION	f_plane_restr	0.008	1987

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 (%)
2.098-2.1219	0.2683	134	0.1967	2523	X-RAY DIFFRACTION	91
2.1219-2.1468	0.2287	140	0.1775	2552	X-RAY DIFFRACTION	91
2.1468-2.173	0.2301	128	0.1721	2603	X-RAY DIFFRACTION	93
2.173-2.2005	0.2524	128	0.1624	2604	X-RAY DIFFRACTION	92
2.2005-2.2294	0.2104	149	0.1605	2581	X-RAY DIFFRACTION	94
2.2294-2.26	0.2167	134	0.1625	2637	X-RAY DIFFRACTION	93
2.26-2.2923	0.194	147	0.1625	2694	X-RAY DIFFRACTION	96
2.2923-2.3265	0.2122	142	0.1598	2684	X-RAY DIFFRACTION	96
2.3265-2.3628	0.211	116	0.1593	2734	X-RAY DIFFRACTION	97
2.3628-2.4015	0.2167	141	0.1603	2800	X-RAY DIFFRACTION	98
2.4015-2.4429	0.2139	163	0.1576	2723	X-RAY DIFFRACTION	99
2.4429-2.4873	0.2096	137	0.1585	2838	X-RAY DIFFRACTION	99
2.4873-2.5351	0.235	137	0.1531	2794	X-RAY DIFFRACTION	99
2.5351-2.5868	0.2174	155	0.1639	2817	X-RAY DIFFRACTION	100
2.5868-2.6431	0.2178	144	0.1648	2804	X-RAY DIFFRACTION	100
2.6431-2.7045	0.2238	152	0.1586	2840	X-RAY DIFFRACTION	100
2.7045-2.7721	0.2262	138	0.1593	2824	X-RAY DIFFRACTION	100
2.7721-2.847	0.2222	136	0.1649	2834	X-RAY DIFFRACTION	100
2.847-2.9307	0.2283	145	0.1661	2845	X-RAY DIFFRACTION	100
2.9307-3.0252	0.2097	145	0.1694	2820	X-RAY DIFFRACTION	100
3.0252-3.1332	0.2159	164	0.1725	2842	X-RAY DIFFRACTION	100
3.1332-3.2585	0.2409	145	0.1706	2843	X-RAY DIFFRACTION	100
3.2585-3.4066	0.2252	143	0.1601	2849	X-RAY DIFFRACTION	100
3.4066-3.5859	0.1988	135	0.1501	2866	X-RAY DIFFRACTION	100
3.5859-3.8102	0.1822	158	0.1377	2856	X-RAY DIFFRACTION	100
3.8102-4.1036	0.1761	164	0.1259	2860	X-RAY DIFFRACTION	100
4.1036-4.5153	0.1424	153	0.1109	2869	X-RAY DIFFRACTION	100
4.5153-5.1657	0.148	136	0.1077	2945	X-RAY DIFFRACTION	100
5.1657-6.497	0.1728	166	0.1485	2919	X-RAY DIFFRACTION	100
6.497-29.6986	0.2017	172	0.1707	3006	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	0.9905	-0.1954	0.2385	0.8898	0.217	1.5145	0.0263	-0.1532	0.1952	0.1958	-0.0572	0.0727	-0.1837	0.0142	0.0602	0.225	-0.0809	0.0523	0.2152	-0.0746	0.2133	55.0855	40.3213	132.7375
2	2.1382	1.186	0.9338	0.5286	0.3577	0.59	0.1431	-0.1279	-0.0215	0.0282	-0.0931	0.0511	0.0093	0.0309	-0.0598	0.1069	-0.0198	0.0221	0.1543	-0.0223	0.2278	47.8084	11.7158	118.9123
3	0.5927	0.4318	0.0383	1.8385	0.0892	1.5657	-0.0035	-0.0283	-0.0839	-0.029	-0.0128	-0.1599	0.124	0.0497	0.0084	0.1052	-0.0443	0.0545	0.1988	-0.0299	0.2013	60.2466	19.1987	118.8955
4	0.7809	-0.4766	-0.4333	1.3801	0.4902	2.3596	0.1744	0.0874	0.094	-0.0548	0.0305	-0.0054	-0.2416	-0.1986	-0.1645	0.1462	0.047	0.0397	0.1442	0.0393	0.2376	18.8824	19.7646	114.7973
5	4.6687	2.3176	-0.3371	1.0825	-0.373	0.1709	0.2048	-0.2566	-0.2083	0.2553	-0.0502	-0.0601	-0.0072	0.1065	-0.1153	0.2922	-0.049	0.074	0.3791	-0.0346	0.2447	38.4422	29.421	147.9786
6	3.0277	-0.3151	1.4359	1.105	0.5701	4.1575	0.1235	-0.2184	0.1294	0.0576	-0.0815	0.028	0.2747	-0.2448	-0.0701	0.1714	-0.0072	0.1133	0.1886	0.0153	0.2509	17.2216	22.0183	137.4018
7	1.0598	-0.163	-0.0179	0.5374	0.8791	2.7051	0.1536	-0.239	0.0054	0.1288	-0.0177	-0.0123	0.0116	-0.0947	-0.0968	0.1865	-0.0135	0.0562	0.209	0.0524	0.2255	17.0663	22.755	139.7674
8	1.1959	0.4796	0.1488	1.5178	-0.6372	3.5419	0.3054	-0.2639	0.0951	-0.105	-0.1448	-0.3542	-0.1564	0.2695	-0.204	0.1862	-0.0201	0.0652	0.2626	-0.0168	0.3106	25.5098	28.7986	140.7752
9	2.6119	0.3275	-0.12	1.3032	-0.134	2.812	0.0602	0.1345	0.3043	0.0351	0.0062	0.0656	-0.3363	-0.0321	-0.076	0.3427	0.0502	0.0414	0.2643	0.0356	0.2391	23.1203	42.2965	174.8533
10	1.1583	-0.4562	0.4443	0.8464	-0.4218	0.4699	0.0498	0.0467	-0.134	0.0964	0.0116	0.2052	-0.0749	-0.0727	-0.0543	0.3198	0.0299	0.0458	0.2423	-0.0075	0.2193	26.0766	20.9007	190.126
11	0.9796	-0.4455	-0.2602	1.7683	-0.3398	1.0647	-0.0352	0.0406	-0.2196	0.1342	-0.005	0.3135	0.0839	-0.0821	0.0346	0.3216	0.0376	0.0561	0.2958	-0.017	0.3167	16.2217	20.2611	190.0981
12	1.2997	0.5792	-0.3959	1.7897	-0.7633	1.3293	0.1446	-0.0976	-0.0231	0.0666	-0.1059	-0.1559	-0.0854	0.1415	-0.0616	0.3485	-0.0015	0.0055	0.2596	-0.0141	0.2454	57.2676	18.1272	194.939
13	3.5068	-2.3733	-0.2685	1.3493	0.0252	0.125	0.12	0.3327	-0.2712	-0.139	-0.0808	0.1475	0.0073	-0.0079	-0.0244	0.3292	-0.0034	0.0374	0.4159	-0.0451	0.266	39.6848	28.4825	163.0534
14	1.9835	0.2846	1.4204	1.324	0.5553	5.7386	-0.0768	0.3175	-0.0805	0.0133	0.0018	-0.1357	0.2039	0.5287	0.0599	0.2974	0.0304	0.0743	0.3243	0.0211	0.2504	63.3192	23.3359	173.9759
15	1.1634	0.0966	0.7468	0.7996	-1.2292	2.5872	-0.0398	0.2213	-0.0688	-0.0671	-0.0634	-0.0891	0.2325	0.062	0.0804	0.3443	0.0392	0.0648	0.2847	-0.0667	0.2397	58.3543	17.8427	169.26
16	0.3703	0.0122	0.6922	1.3338	0.8644	2.6849	-0.0355	0.2519	-0.1654	0.1188	-0.118	0.1507	-0.1022	-0.1812	0.1309	0.3293	0.0463	0.0503	0.3411	-0.0216	0.2583	54.8559	30.3623	167.9296

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 431:476)

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