PDB-7puq: CARM1 in complex with EML982

ID or keywords:

Entry

Database: PDB / ID: 7puq

Title

CARM1 in complex with EML982

Components

Histone-arginine methyltransferase CARM1

Keywords

TRANSCRIPTION / PROTEIN ARGININE N-METHYLTRANSFERASE / PRMT4 / CARM1 / INHIBITOR

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: 2.09 Å

Authors

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

Funding support

1items

Citation

Journal: J.Med.Chem. / Year: 2022
Title: Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction- ...
Authors: Iannelli, G. / Milite, C. / Marechal, N. / Cura, V. / Bonnefond, L. / Troffer-Charlier, N. / Feoli, A. / Rescigno, D. / Wang, Y. / Cipriano, A. / Viviano, M. / Bedford, M.T. / Cavarelli, J. ...

History

Deposition	Sep 30, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 11, 2022	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Sep 21, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7puq.cif.gz	796.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7puq.ent.gz	682.9 KB	Display	PDB format
PDBx/mmJSON format	7puq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7puq_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	7puq_full_validation.pdf.gz	1.5 MB	Display
Data in XML	7puq_validation.xml.gz	54.4 KB	Display
Data in CIF	7puq_validation.cif.gz	75.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pu/7puq ftp://data.pdbj.org/pub/pdb/validation_reports/pu/7puq	HTTPS FTP

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Related structure data

Related structure data	7nudC 7nueC 7p2rC 7ppqC 7ppyC 7pu8C 7pucC 7pv6C 5ih3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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 author&software

Unit cell

Length a, b, c (Å)	75.128, 98.694, 207.778
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	C-710- HOH

#1: Protein	Histone-arginine methyltransferase CARM1 / Coactivator-associated arginine methyltransferase 1 / Protein arginine N-methyltransferase 4 Mass: 40793.406 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 aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: Q9WVG6, type I protein arginine methyltransferase
#2: Chemical	ChemComp-867 / methyl 6-[4-[[~{N}-[3-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]propyl]carbamimidoyl]amino]butylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate Mass: 650.686 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₀H₃₈N₁₀O₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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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: 47.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 12% PEG 3350, 0.1 M NaCl, 0.1 M TrisHCl pH8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 8, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.09→48.01 Å / Num. obs: 92014 / % possible obs: 99.5 % / Redundancy: 13.4 % / B_iso Wilson estimate: 42.5 Å² / CC_1/2: 1 / R_merge(I) obs: 0.085 / R_pim(I) all: 0.024 / R_rim(I) all: 0.089 / Net I/σ(I): 17.8
Reflection shell	Resolution: 2.09→2.12 Å / Redundancy: 12 % / R_merge(I) obs: 1.33 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4053 / CC_1/2: 0.831 / R_pim(I) all: 0.386 / R_rim(I) all: 1.387 / % possible all: 90.2

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3

Resolution: 2.09→48.01 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2174	4551	4.96 %
R_work	0.1811	87284	-
obs	0.1829	91835	99.34 %

Solvent computation

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

Displacement parameters

B_iso max: 136.68 Å² / B_iso mean: 53.2704 Å² / B_iso min: 25.81 Å²

Refinement step

Cycle: final / Resolution: 2.09→48.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11001	0	410	442	11853
B_iso mean	-	-	68.42	48.59	-
Num. residues	-	-	-	-	1371

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.09-2.11	0.3091	118	0.2922	2429	2547	85
2.11-2.14	0.3226	144	0.261	2931	3075	100
2.14-2.16	0.2846	158	0.2446	2865	3023	100
2.16-2.19	0.2887	149	0.2488	2893	3042	100
2.19-2.22	0.3094	164	0.2308	2883	3047	100
2.22-2.25	0.2687	158	0.2234	2873	3031	100
2.25-2.28	0.2487	154	0.2175	2881	3035	100
2.28-2.32	0.2513	134	0.2189	2859	2993	100
2.32-2.35	0.2781	149	0.2081	2957	3106	100
2.35-2.39	0.277	136	0.2056	2884	3020	100
2.39-2.43	0.2264	176	0.2026	2883	3059	100
2.43-2.48	0.2277	141	0.1991	2908	3049	100
2.48-2.52	0.3112	143	0.2121	2891	3034	100
2.52-2.58	0.2647	158	0.2289	2905	3063	100
2.58-2.63	0.2822	146	0.215	2904	3050	100
2.63-2.69	0.2639	161	0.1976	2896	3057	100
2.69-2.76	0.2258	130	0.1973	2940	3070	100
2.76-2.83	0.2596	161	0.1952	2892	3053	100
2.83-2.92	0.2486	149	0.1893	2929	3078	100
2.92-3.01	0.2256	143	0.2012	2943	3086	100
3.01-3.12	0.2403	165	0.2148	2893	3058	100
3.12-3.24	0.2264	147	0.2141	2930	3077	100
3.24-3.39	0.2595	153	0.1973	2932	3085	100
3.39-3.57	0.2376	132	0.1768	2977	3109	100
3.57-3.79	0.2019	159	0.1625	2932	3091	100
3.79-4.09	0.1737	176	0.1515	2935	3111	100
4.09-4.5	0.1522	162	0.132	2979	3141	100
4.5-5.15	0.1598	137	0.1289	3003	3140	100
5.15-6.48	0.1814	171	0.1713	3015	3186	100
6.48-48.01	0.2075	177	0.1753	3142	3319	99

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	2.2092	-0.4916	0.0511	1.0229	0.0928	2.6385	-0.0163	-0.2241	0.2815	0.1167	-0.0389	-0.0136	-0.2613	0.0947	0.0589	0.3934	-0.07	0.0355	0.3115	-0.0521	0.3392	55.156	40.2835	134.0185
2	2.0871	0.7224	0.8764	-0.0486	0.3408	0.9454	0.1175	-0.0496	-0.0616	0.0386	-0.0479	0.0669	0.0518	0.0956	-0.0735	0.2794	0.0003	0.0093	0.2092	-0.0017	0.3519	46.151	12.0493	118.2711
3	2.0501	0.3242	0.1593	4.0053	1.0722	1.6461	-0.0675	0.0537	-0.0537	-0.1115	-0.0077	-0.2688	-0.0743	0.1381	0.0607	0.2565	-0.0433	0.0198	0.247	-0.0038	0.2597	61.5207	20.796	122.715
4	1.1548	0.5057	-0.4399	2.5584	-0.5351	2.2241	-0.0181	-0.0039	-0.1125	-0.1814	-0.0016	-0.2217	0.2636	0.2447	0.0025	0.2093	-0.0098	0.0339	0.2509	-0.0006	0.3051	62.1581	18.8704	121.1666
5	3.1485	-1.3462	-0.0454	4.6962	1.1621	1.771	0.0895	0.064	-0.2313	-0.0921	-0.2203	0.2249	0.254	-0.2762	0.1171	0.3328	-0.0913	0.0493	0.2667	0.008	0.2739	53.2493	17.362	115.3913
6	1.8505	-0.0329	0.0916	1.0008	1.4163	3.6385	0.1178	0.0328	0.1396	-0.1444	0.0018	0.075	-0.3265	-0.2633	-0.0956	0.3233	0.0649	0.035	0.239	0.0637	0.3255	19.6811	19.6839	114.8781
7	3.0012	1.4541	0.8073	0.8393	0.6843	0.8532	0.2916	-0.2836	-0.0396	0.1999	-0.1057	-0.0114	-0.0621	0.0216	-0.1621	0.4247	-0.0118	0.0561	0.4057	0.0242	0.317	32.8454	27.2084	144.28
8	4.9209	0.0238	1.549	1.7017	0.8899	4.5268	0.2455	-0.2793	-0.2109	0.1887	-0.1335	0.1266	0.1844	-0.2955	-0.1503	0.3772	-0.0119	0.0734	0.2921	0.0006	0.3108	17.0904	21.6891	138.0228
9	1.6829	0.1458	0.6748	1.3545	1.3033	3.9199	0.1752	-0.294	0.0039	0.1983	-0.0347	0.0565	0.001	-0.4666	-0.1417	0.2916	0.0009	0.0423	0.3631	0.0785	0.2878	16.9061	22.4516	140.4785
10	1.6448	0.2637	0.762	1.523	-1.247	4.9105	0.2486	-0.1264	0.1198	0.0188	0.0367	-0.0597	-0.4238	-0.0249	-0.3138	0.32	-0.0483	0.0576	0.3304	-0.026	0.3239	24.4745	29.9105	142.1323
11	2.4896	0.2389	0.1726	1.121	-0.4851	2.8344	0.0034	0.1231	0.2938	-0.0047	-0.0028	0.0724	-0.3712	-0.1914	-0.0058	0.4437	0.0753	0.0595	0.4113	0.0195	0.3284	22.4095	41.4003	177.9255
12	1.6944	-0.6999	0.5989	0.719	-0.3942	1.084	0.1035	0.0407	-0.0803	0.0433	-0.055	0.1011	-0.0547	-0.1894	-0.0503	0.3142	-0.0085	0.0265	0.3203	-0.0034	0.3008	29.7068	12.5894	193.7601
13	1.7681	0.2	-0.1221	3.1215	-0.6685	1.2873	-0.0047	-0.0691	-0.0417	-0.0179	0.1113	0.2713	-0.1897	-0.2591	-0.1012	0.3337	0.0897	0.0512	0.4223	-0.0155	0.2788	14.8619	22.2287	189.0177
14	1.234	-0.6782	-0.7761	2.0536	-0.0942	1.4962	-0.0036	0.0697	-0.1416	0.097	0.0237	0.369	0.0481	-0.3373	0.0061	0.2953	0.0208	0.0467	0.4195	-0.0298	0.3603	14.0697	20.4208	190.4633
15	2.9377	1.9284	0.4315	4.9695	-1.2671	0.761	0.037	0.2714	-0.0559	-0.037	-0.05	-0.0441	0.1004	0.0533	0.0323	0.3746	0.0805	0.0484	0.3807	-0.036	0.3507	22.7883	18.3738	196.4304
16	1.6389	-0.1931	-0.3026	2.5774	-0.5688	2.7375	0.101	-0.0982	0.0559	0.1186	-0.09	-0.1265	-0.1186	0.1781	-0.015	0.2924	-0.0545	0.0204	0.336	-0.0335	0.2796	56.7238	18.0601	197.1024
17	2.1762	-0.8132	0.5432	0.573	-0.2857	0.4901	0.3243	0.2697	0.029	-0.2055	-0.1984	-0.0471	0.1129	-0.1677	-0.0906	0.4226	-0.0077	0.0575	0.5217	0.0006	0.3175	43.9529	26.9579	167.646
18	4.3235	0.5435	1.6958	2.0544	0.3354	4.9502	0.079	0.3737	-0.1582	-0.2392	-0.0102	-0.1911	0.2991	0.3693	-0.0302	0.3596	0.0463	0.0545	0.3725	0.0421	0.3184	59.1793	20.2423	173.8898
19	1.2311	-0.1987	1.0623	1.0924	-1.2301	2.6896	0.1433	0.3741	-0.0853	-0.2754	-0.1345	-0.0995	0.1039	0.4822	0.0049	0.3608	0.0201	0.0518	0.479	-0.0526	0.352	59.3465	20.9775	171.4533
20	1.6823	-0.5822	0.2434	1.6953	0.9203	3.3383	0.3385	0.393	0.0219	-0.14	-0.1625	0.0523	-0.3886	-0.2852	-0.221	0.3985	0.0249	0.0083	0.4779	0.0088	0.3397	52.4081	28.9546	169.8024

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 136:282)	A	136 - 282
2	X-RAY DIFFRACTION	2	(chain A and resid 283:336)	A	283 - 336
3	X-RAY DIFFRACTION	3	(chain A and resid 337:365)	A	337 - 365
4	X-RAY DIFFRACTION	4	(chain A and resid 366:445)	A	366 - 445
5	X-RAY DIFFRACTION	5	(chain A and resid 446:478)	A	446 - 478
6	X-RAY DIFFRACTION	6	(chain B and resid 135:282)	B	135 - 282
7	X-RAY DIFFRACTION	7	(chain B and resid 283:336)	B	283 - 336
8	X-RAY DIFFRACTION	8	(chain B and resid 337:365)	B	337 - 365
9	X-RAY DIFFRACTION	9	(chain B and resid 366:445)	B	366 - 445
10	X-RAY DIFFRACTION	10	(chain B and resid 446:477)	B	446 - 477
11	X-RAY DIFFRACTION	11	(chain C and resid 136:282)	C	136 - 282
12	X-RAY DIFFRACTION	12	(chain C and resid 283:336)	C	283 - 336
13	X-RAY DIFFRACTION	13	(chain C and resid 337:365)	C	337 - 365
14	X-RAY DIFFRACTION	14	(chain C and resid 366:445)	C	366 - 445
15	X-RAY DIFFRACTION	15	(chain C and resid 446:478)	C	446 - 478
16	X-RAY DIFFRACTION	16	(chain D and resid 136:282)	D	136 - 282
17	X-RAY DIFFRACTION	17	(chain D and resid 283:336)	D	283 - 336
18	X-RAY DIFFRACTION	18	(chain D and resid 337:365)	D	337 - 365
19	X-RAY DIFFRACTION	19	(chain D and resid 366:445)	D	366 - 445
20	X-RAY DIFFRACTION	20	(chain D and resid 446:477)	D	446 - 477

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