PDB-7puc: CARM1 in complex with EML981

ID or keywords:

Entry

Database: PDB / ID: 7puc

Title

CARM1 in complex with EML981

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

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.19 Å

Authors

Marechal, N. / Cura, V. / Bonnefond, L. / Troffer-Charlier, N. / 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 29, 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	7puc.cif.gz	787.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7puc.ent.gz	675.2 KB	Display	PDB format
PDBx/mmJSON format	7puc.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/pu/7puc ftp://data.pdbj.org/pub/pdb/validation_reports/pu/7puc	HTTPS FTP

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Related structure data

Related structure data	7nudC 7nueC 7p2rC 7ppqC 7ppyC 7pu8C 7puqC 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)	75.322, 98.943, 208.195
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	A-657- HOH

#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 aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: Q9WVG6, type I protein arginine methyltransferase
#2: Chemical	ChemComp-85U / methyl 6-[4-[[~{N}-[(~{E})-3-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]prop-2-enyl]carbamimidoyl]amino]butylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate Mass: 648.670 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₀H₃₆N₁₀O₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.37 Å³/Da / Density % sol: 48.19 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 15% PEG 3350, 200mM AMMONIUM SULFATE, 100mM TRIS HCL 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: 2.19→48.13 Å / Num. obs: 80457 / % possible obs: 99.2 % / Redundancy: 13.3 % / B_iso Wilson estimate: 45.3 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.158 / R_pim(I) all: 0.063 / R_rim(I) all: 0.164 / Net I/σ(I): 11.1
Reflection shell	Resolution: 2.19→2.23 Å / Redundancy: 11.7 % / R_merge(I) obs: 2.821 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3971 / CC_1/2: 0.511 / R_pim(I) all: 0.843 / R_rim(I) all: 2.95 / % possible all: 87

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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: 2.19→48.13 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 27.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2305	3981	4.96 %
R_work	0.2023	76273	-
obs	0.2037	80254	99.02 %

Solvent computation

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

Displacement parameters

B_iso max: 179.56 Å² / B_iso mean: 57.8876 Å² / B_iso min: 23.77 Å²

Refinement step

Cycle: final / Resolution: 2.19→48.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10993	0	342	223	11558
B_iso mean	-	-	91.78	61.73	-
Num. residues	-	-	-	-	1370

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 28

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.19-2.22	0.4022	122	0.3953	2178	2300	79
2.22-2.24	0.3531	154	0.3299	2655	2809	100
2.24-2.27	0.3403	142	0.322	2706	2848	100
2.27-2.3	0.3154	141	0.3004	2736	2877	100
2.3-2.34	0.33	140	0.2935	2720	2860	100
2.34-2.37	0.3051	116	0.2794	2726	2842	100
2.37-2.41	0.305	132	0.265	2705	2837	100
2.41-2.45	0.2471	154	0.2464	2698	2852	100
2.45-2.49	0.3074	148	0.2524	2735	2883	100
2.49-2.54	0.3166	122	0.2616	2744	2866	100
2.54-2.59	0.265	155	0.2661	2686	2841	100
2.59-2.64	0.3198	136	0.2471	2719	2855	100
2.64-2.7	0.2706	154	0.2264	2728	2882	100
2.7-2.76	0.2629	127	0.2166	2716	2843	100
2.76-2.83	0.227	142	0.2207	2749	2891	100
2.83-2.9	0.2434	141	0.2171	2720	2861	100
2.9-2.99	0.2699	124	0.2288	2745	2869	100
2.99-3.09	0.2744	150	0.2438	2712	2862	100
3.09-3.2	0.2949	155	0.2638	2751	2906	100
3.2-3.32	0.2938	136	0.2397	2717	2853	100
3.32-3.47	0.2608	132	0.2082	2780	2912	100
3.47-3.66	0.2246	137	0.1899	2761	2898	100
3.66-3.89	0.1769	157	0.1779	2747	2904	100
3.89-4.19	0.209	155	0.1597	2767	2922	100
4.19-4.61	0.1455	148	0.1407	2782	2930	100
4.61-5.27	0.1757	131	0.1377	2826	2957	100
5.27-6.64	0.1955	157	0.1777	2825	2982	100
6.64-48.13	0.1945	173	0.1729	2939	3112	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	1.6332	-0.0957	-0.1438	1.4571	0.0986	1.7059	-0.0171	-0.1961	0.2246	0.176	0.0188	0.0317	-0.1585	0.0367	0	0.4001	-0.059	0.0289	0.3244	-0.0636	0.409	55.2201	40.3436	134.3528
2	0.8376	0.0743	0.5653	-0.2078	0.3454	0.6005	0.1381	-0.0105	-0.0804	0.1304	-0.0216	-0.0251	0.0035	0.122	-0	0.2866	-0.0267	0.0095	0.2314	0.0095	0.4266	46.2609	12.0881	118.5106
3	0.3244	0.1358	-0.131	0.7646	0.8425	0.6371	-0.1042	0.0536	-0.0857	-0.0147	0.0306	-0.0791	-0.0541	0.1788	-0	0.3457	-0.0779	0.0313	0.3849	0.0192	0.4854	61.6638	20.8475	122.9407
4	1.0357	0.2614	-0.1802	1.7044	-0.3713	1.5182	-0.0431	-0.0128	-0.1248	-0.149	-0.0354	-0.1588	0.1787	0.1847	0	0.3207	-0.0343	0.0299	0.3306	-0.0208	0.4231	62.2764	18.9282	121.4182
5	0.8106	0.7493	0.7111	0.7079	0.1378	0.5571	-0.0451	-0.0877	-0.173	0.0344	-0.0243	0.1001	0.1593	0.0316	0	0.4282	-0.0572	0.0724	0.3482	0.0174	0.3936	53.3334	17.4179	115.6047
6	1.1362	-0.2086	-0.063	1.0417	0.6984	2.9443	0.1837	0.0286	0.0404	-0.0715	0.0082	0.0459	-0.2146	-0.2582	0	0.3471	0.0567	0.043	0.2726	0.0616	0.4303	19.7199	19.6578	115.0668
7	0.4669	0.6884	-0.7943	0.5099	0.0671	0.4525	0.3527	-0.3281	-0.0229	0.2088	-0.1406	0.0192	-0.1667	0.0403	-0	0.5165	0.0318	0.0635	0.4342	0.0208	0.4266	32.8334	27.2719	144.5534
8	0.7707	0.3953	0.0623	0.5951	1.0235	0.6246	0.1915	-0.2304	0.1375	0.1947	-0.1541	0.0298	-0.0127	-0.1851	-0	0.4728	0.006	0.0617	0.5243	0.0708	0.5184	17.1789	21.7541	138.2355
9	1.6536	0.1021	-0.1637	0.5602	0.4831	1.5451	0.1158	-0.2468	-0.0136	0.1954	0.063	0.1043	-0.0923	-0.2233	-0	0.4505	0.0263	0.0528	0.4542	0.092	0.4133	16.957	22.3976	140.7133
10	0.6364	0.1102	0.9228	0.6135	0.3108	0.3162	0.0892	-0.3122	-0.1106	0.0872	-0.1814	-0.0515	-0.2101	0.3341	0	0.552	0.0271	0.1247	0.5217	0.0515	0.467	24.5472	30.1338	142.3704
11	1.7448	0.3223	-0.6087	1.022	-0.0718	1.7414	0.1222	0.1502	0.2228	-0.0806	-0.0148	-0.0161	-0.4369	-0.0994	0	0.5857	0.1118	0.0784	0.5002	0.0302	0.4055	22.3731	41.4105	178.1816
12	0.4394	-0.2849	0.056	0.27	-0.1157	0.9779	0.0441	0.0045	-0.0809	0.0634	-0.0153	0.123	-0.1141	-0.1839	-0	0.4025	-0.0007	0.0087	0.3769	-0.0224	0.4398	29.7408	12.5858	194.1248
13	0.5933	-0.1274	-0.1817	0.5271	-0.441	0.7207	-0.0448	0.089	-0.1891	0.0121	0.0669	0.1371	-0.2009	-0.2606	-0	0.4647	0.0869	0.0236	0.5385	-0.0261	0.502	14.8716	22.2459	189.3963
14	1.1263	-0.4625	-1.0331	0.9891	0.6398	0.7894	-0.0314	0.0943	-0.1651	0.184	-0.0574	0.1977	-0.0502	-0.3065	-0	0.4358	0.0526	0.0412	0.5367	-0.0126	0.4533	14.0732	20.378	190.8963
15	0.4619	-0.6458	0.4044	0.7192	-0.161	0.3908	-0.1497	0.2643	-0.1404	0.0709	0.0977	0.0416	0.1772	-0.1951	0	0.5583	0.0481	0.1018	0.5255	0.0053	0.4665	22.6743	18.5998	197.3786
16	1.4302	0.4702	-0.3392	1.8239	-0.0399	2.2444	0.196	-0.1143	0.0329	0.1487	-0.1178	-0.0849	-0.1793	0.2247	0	0.3965	-0.0794	0.0173	0.4385	-0.0388	0.3972	56.8409	18.3457	197.5115
17	0.3125	-0.1993	-0.2178	0.226	-0.0323	0.2859	0.2308	0.1724	-0.0811	-0.1474	-0.0923	-0.0036	-0.0567	-0.023	0	0.5231	-0.0264	0.066	0.6091	-0.0298	0.4503	43.9151	26.9702	167.9083
18	0.6509	-0.0507	-0.1012	0.5222	-0.5867	0.3607	-0.0142	0.1399	-0.0403	-0.246	-0.1082	-0.07	0.0976	0.2192	0	0.5235	0.0131	0.0401	0.6946	-0.0292	0.4936	59.2648	20.3034	174.218
19	1.044	0.0156	0.1934	0.4908	-0.8518	0.8446	0.1549	0.2792	-0.0008	-0.1099	-0.0977	-0.0489	0.0241	0.2805	0	0.5285	0.0109	0.0421	0.6205	-0.0899	0.4505	59.4135	21.0295	171.7786
20	0.1899	-0.2761	0.5717	0.3132	-0.1008	0.2531	0.1802	0.4931	-0.0594	-0.1033	-0.1847	0.2457	-0.3575	-0.3289	0	0.6222	0.0197	0.1159	0.6491	-0.0196	0.4846	52.8801	29.9498	169.922

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 446:477)	C	446 - 477
16	X-RAY DIFFRACTION	16	(chain D and resid 135:282)	D	135 - 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 446:476)	D	446 - 476

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