PDB-5isi: Crystal structure of mouse CARM1 in complex with inhibitor SA0920...

ID or keywords:

Entry

Database: PDB / ID: 5isi

Title

Crystal structure of mouse CARM1 in complex with inhibitor SA0920 (5'-amino-5'-deoxyadenosine)

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 / negative regulation of dendrite development / Cytoprotection by HMOX1 / type I protein arginine methyltransferase ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.74 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 SA0920 (5'-amino-5'-deoxyadenosine)
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 / citation / database_2 / pdbx_initial_refinement_model Item: _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5isi.cif.gz	780.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5isi.ent.gz	668.2 KB	Display	PDB format
PDBx/mmJSON format	5isi.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/is/5isi ftp://data.pdbj.org/pub/pdb/validation_reports/is/5isi	HTTPS FTP

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Related structure data

Related structure data	5ih3S S: Starting model for refinement
Similar structure data	5ish-d 6s7c-d 2y1w-d 5is7-d 5tbh-d 6s7a-d 5isa-d 6s79-d 5k8x-d 5k8v-d 5lv2-1 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

165 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)	74.736, 98.522, 207.054
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#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
#2: Chemical	ChemComp-5N5 / 5'-amino-5'-deoxyadenosine Mass: 266.257 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₆O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-DXE / 1,2-DIMETHOXYETHANE / Dimethoxyethane Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.33 Å³/Da / Density % sol: 47.27 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris-HCl pH 8.0 100 mM PEG 2000 MME 16% NaCl 67 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: Mar 17, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9801 Å / Relative weight: 1
Reflection	Resolution: 2.74→20 Å / Num. obs: 39458 / % possible obs: 98.9 % / Redundancy: 5.1 % / B_iso Wilson estimate: 56.2 Å² / R_sym value: 0.091 / Net I/σ(I): 17.5
Reflection shell	Resolution: 2.74→2.9 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.6 / % possible all: 98.4

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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: 2.74→19.709 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.32

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2137	1976	5.01 %	Random selection
R_work	0.1747	-	-	-
obs	0.1767	39412	95.83 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.74→19.709 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10997	0	112	15	11124

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	11389
X-RAY DIFFRACTION	f_angle_d	0.847	15426
X-RAY DIFFRACTION	f_dihedral_angle_d	18.554	4164
X-RAY DIFFRACTION	f_chiral_restr	0.039	1690
X-RAY DIFFRACTION	f_plane_restr	0.003	1959

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 (%)
2.7351-2.8033	0.2741	80	0.2408	1488	X-RAY DIFFRACTION	55
2.8033-2.8789	0.2986	143	0.2335	2707	X-RAY DIFFRACTION	98
2.8789-2.9633	0.3145	123	0.2393	2701	X-RAY DIFFRACTION	99
2.9633-3.0586	0.2763	152	0.2217	2717	X-RAY DIFFRACTION	99
3.0586-3.1675	0.2718	152	0.2173	2707	X-RAY DIFFRACTION	98
3.1675-3.2938	0.2405	141	0.2128	2720	X-RAY DIFFRACTION	98
3.2938-3.4429	0.2435	131	0.1948	2736	X-RAY DIFFRACTION	99
3.4429-3.6234	0.2396	133	0.193	2752	X-RAY DIFFRACTION	99
3.6234-3.8489	0.2111	153	0.1731	2743	X-RAY DIFFRACTION	99
3.8489-4.1435	0.2213	161	0.1591	2798	X-RAY DIFFRACTION	100
4.1435-4.5558	0.1725	146	0.1442	2778	X-RAY DIFFRACTION	100
4.5558-5.2044	0.19	130	0.136	2840	X-RAY DIFFRACTION	100
5.2044-6.5174	0.1989	160	0.1739	2837	X-RAY DIFFRACTION	100
6.5174-19.7092	0.1602	171	0.1568	2912	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	1.4765	-0.4129	0.0133	0.8157	-0.1957	1.9948	0.0806	-0.0708	0.1608	-0.0194	-0.0905	0.0178	-0.124	0.0387	0.0002	0.4766	-0.0616	0.0304	0.4305	-0.0805	0.4398	55.1083	40.5107	133.342
2	1.1925	-0.0922	0.12	0.0249	0.1122	0.5004	0.1428	-0.0255	-0.0231	0.1504	-0.0405	0.0222	0.053	0.1156	0.0001	0.2796	-0.0187	0.0015	0.2799	0.0067	0.3957	47.8367	11.9569	119.3908
3	1.4208	0.4411	0.2345	2.5664	0.261	1.9675	-0.0256	-0.0298	-0.0943	-0.1714	0.0834	-0.1595	0.094	0.0473	-0.0002	0.273	-0.0391	0.0696	0.3569	0.0051	0.3687	60.3661	19.3342	119.2556
4	1.3908	-0.2761	-0.8301	1.4676	0.6261	2.0838	0.098	0.0728	0.0782	0.0681	0.0765	-0.0011	-0.32	-0.0945	0.0003	0.3863	0.0563	0.0344	0.3488	0.0315	0.3967	18.9411	19.7327	115.1406
5	1.0399	0.5455	0.1337	0.1733	0.0416	-0.038	0.3827	-0.3112	-0.3661	0.4906	-0.1996	-0.0678	-0.0595	0.1413	0.0005	0.5551	-0.0949	0.0337	0.6398	0.0169	0.4752	38.5157	29.3401	148.7394
6	0.3133	0.0437	0.1524	0.9069	1.1459	1.4387	-0.0121	-0.2429	0.1559	0.0583	-0.0421	-0.261	0.028	-0.2387	0.0004	0.4872	-0.0139	0.0992	0.5374	0.0543	0.5564	17.1946	21.8835	138.0894
7	1.4149	0.5028	-0.3747	0.4793	0.4624	1.2417	0.1356	-0.2916	-0.0558	0.0558	0.015	-0.0167	-0.044	-0.0216	0.0002	0.4402	0.0146	0.0275	0.4676	0.0118	0.3932	17.0581	22.6257	140.4198
8	0.4528	0.5008	0.5587	0.9845	0.2915	0.8897	0.1128	-0.0718	0.0361	-0.1075	-0.1099	-0.3296	-0.0397	0.0441	-0.0009	0.5591	-0.0172	0.0948	0.6461	-0.0201	0.5781	24.6498	30.0973	141.8979
9	1.2578	0.1363	-0.0123	1.1141	-0.096	2.1795	0.0317	0.0752	0.2239	0.1639	-0.0214	0.0427	-0.1022	-0.037	-0	0.5194	0.0204	0.0263	0.4917	0.0316	0.4627	23.1336	42.5735	175.418
10	0.5675	-0.4504	0.4465	0.8188	-0.4796	0.2567	0.0808	0.0261	-0.2276	0.0734	0.0419	0.2402	-0.0633	-0.1211	0.0001	0.5044	0.0422	0.0286	0.4184	-0.0014	0.4448	26.0786	21.2983	190.832
11	0.7746	-0.4887	-0.0509	2.0166	-0.5041	1.3469	-0.0787	0.1071	-0.2106	0.162	0.1607	0.3593	0.0588	-0.164	0.0006	0.4701	0.0387	0.0934	0.4455	-0.0268	0.5113	16.2101	20.3187	190.8601
12	1.6272	0.7114	-0.0487	1.2581	-0.2453	1.1144	0.0613	-0.0077	-0.056	-0.02	-0.0346	-0.136	-0.1812	0.0328	0	0.5451	-0.024	-0.0142	0.4254	0.0222	0.4261	57.2726	18.1323	195.6996
13	0.7813	-0.567	0.1439	0.3115	-0.0588	-0.0189	0.2163	0.2542	-0.2986	-0.4652	-0.1067	0.1323	0.0379	0.0115	0.0013	0.5428	0.0658	0.0111	0.6546	-0.0609	0.5138	39.7545	28.3218	163.4534
14	0.673	0.0236	-0.0654	0.5274	-0.5588	0.5844	-0.1286	0.1373	-0.1085	0.2305	0.0023	0.218	0.0206	0.5665	-0.0026	0.62	0.0108	0.027	0.6355	-0.0561	0.6029	63.7193	23.3166	174.9857
15	0.531	0.1376	0.3453	0.7206	-0.4655	0.8189	0.1934	0.2636	-0.2047	-0.1131	-0.0792	-0.0479	0.2066	0.2467	-0	0.5595	0.0374	0.0192	0.5734	-0.0516	0.4969	58.4937	17.5267	169.7651
16	0.7173	-0.0172	0.8205	0.4356	-0.1522	0.9447	0.0217	0.2319	-0.2046	0.0231	-0.222	0.1304	-0.1183	-0.3193	-0.0024	0.5509	0.0366	0.0484	0.639	-0.0594	0.4916	54.1312	29.0715	168.7887

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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