PDB-5ih3: Crystal structure of mouse CARM1 in complex with SAH at 1.8 Angst...

ID or keywords:

Entry

Database: PDB / ID: 5ih3

Title

Crystal structure of mouse CARM1 in complex with SAH at 1.8 Angstroms resolution

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: 1.77 Å

Authors

Cura, V. / Marechal, N. / Mailliot, J. / Troffer-Charlier, N. / Hassenboehler, P. / Wurtz, J.M. / Bonnefond, L. / Cavarelli, J.

Funding support

France, 1items

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	Feb 29, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 29, 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	5ih3.cif.gz	812.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ih3.ent.gz	691.5 KB	Display	PDB format
PDBx/mmJSON format	5ih3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ih3_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5ih3_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5ih3_validation.xml.gz	59.9 KB	Display
Data in CIF	5ih3_validation.cif.gz	87.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ih/5ih3 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/5ih3	HTTPS FTP

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Related structure data

Related structure data	5iseC 3b3fS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6arv-d 4ikp-d 6s74-d 6s7b-d 5tbh-d 5isb-d 5is9-d 5tbi-d 6s71-d 5u4x-d 5dxj-d 5is6-d 6izq-d 5k8w-d 5ise-d 5isf-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 author&software

Unit cell

Length a, b, c (Å)	74.628, 97.920, 204.955
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	C-796- HOH

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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 / Fragment: UNP residues 130-487 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 / Fragment: UNP residues 130-487
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, 1078 molecules

#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: 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
#7: Chemical	ChemComp-DXE / 1,2-DIMETHOXYETHANE Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1051 / 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: 2.29 Å³/Da / Density % sol: 46.38 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris-HCl pH 8.0 100 mM, PEG 2000 MME 19%, NaCl 167 mM PH range: 8

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9304 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9304 Å / Relative weight: 1
Reflection	Resolution: 1.77→47.62 Å / Num. all: 146548 / Num. obs: 146611 / % possible obs: 99.9 % / Redundancy: 7.3 % / B_iso Wilson estimate: 20.8 Å² / R_merge(I) obs: 0.129 / Net I/σ(I): 11.2
Reflection shell	Resolution: 1.77→1.8 Å / Redundancy: 6.8 % / R_merge(I) obs: 1.396 / Mean I/σ(I) obs: 1.5 / % possible all: 98.6

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Processing

Software

Name	Version	Classification
PHENIX	dev_1951	refinement
XDS		data reduction
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3B3F

3b3f

Resolution: 1.77→47.62 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.75 / Phase error: 19.77

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1905	7268	4.96 %	Random selection
R_work	0.164	-	-	-
obs	0.1653	146548	99.83 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 31 Å²

Refinement step

Cycle: LAST / Resolution: 1.77→47.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10989	0	249	1051	12289

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	11587
X-RAY DIFFRACTION	f_angle_d	1.158	15655
X-RAY DIFFRACTION	f_dihedral_angle_d	14.534	4253
X-RAY DIFFRACTION	f_chiral_restr	0.052	1703
X-RAY DIFFRACTION	f_plane_restr	0.006	2040

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 (%)
1.77-1.7901	0.3865	470	0.3482	8663	X-RAY DIFFRACTION	97
1.7901-1.8112	0.3131	476	0.3064	8957	X-RAY DIFFRACTION	100
1.8112-1.8333	0.3042	446	0.2866	8918	X-RAY DIFFRACTION	100
1.8333-1.8565	0.2881	420	0.2805	9055	X-RAY DIFFRACTION	100
1.8565-1.8809	0.3013	487	0.2785	8939	X-RAY DIFFRACTION	100
1.8809-1.9067	0.2871	506	0.2711	8904	X-RAY DIFFRACTION	100
1.9067-1.9339	0.2744	431	0.2461	8969	X-RAY DIFFRACTION	100
1.9339-1.9628	0.2505	447	0.2215	9043	X-RAY DIFFRACTION	100
1.9628-1.9935	0.2098	464	0.2057	8932	X-RAY DIFFRACTION	100
1.9935-2.0261	0.2247	506	0.1976	8920	X-RAY DIFFRACTION	100
2.0261-2.0611	0.2152	514	0.1925	8905	X-RAY DIFFRACTION	100
2.0611-2.0986	0.2086	414	0.1849	8995	X-RAY DIFFRACTION	100
2.0986-2.1389	0.2135	467	0.1781	9035	X-RAY DIFFRACTION	100
2.1389-2.1826	0.2067	482	0.1684	8932	X-RAY DIFFRACTION	100
2.1826-2.23	0.2167	504	0.1624	8913	X-RAY DIFFRACTION	100
2.23-2.2819	0.1796	466	0.1589	8941	X-RAY DIFFRACTION	100
2.2819-2.339	0.1748	430	0.1501	9016	X-RAY DIFFRACTION	100
2.339-2.4022	0.1883	480	0.1516	8935	X-RAY DIFFRACTION	100
2.4022-2.4729	0.1831	460	0.1468	8943	X-RAY DIFFRACTION	100
2.4729-2.5527	0.1784	475	0.1425	8982	X-RAY DIFFRACTION	100
2.5527-2.6439	0.1931	471	0.1501	8919	X-RAY DIFFRACTION	100
2.6439-2.7498	0.1806	449	0.144	8999	X-RAY DIFFRACTION	100
2.7498-2.8749	0.1865	494	0.1511	8988	X-RAY DIFFRACTION	100
2.8749-3.0265	0.177	440	0.1519	8941	X-RAY DIFFRACTION	100
3.0265-3.216	0.1855	484	0.1498	8927	X-RAY DIFFRACTION	100
3.216-3.4643	0.1731	434	0.15	8990	X-RAY DIFFRACTION	100
3.4643-3.8128	0.1657	481	0.1398	8949	X-RAY DIFFRACTION	100
3.8128-4.3642	0.1495	506	0.122	8940	X-RAY DIFFRACTION	100
4.3642-5.4971	0.1455	439	0.1223	8961	X-RAY DIFFRACTION	100
5.4971-47.6374	0.164	502	0.1682	8842	X-RAY DIFFRACTION	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	0.5009	-0.2481	0.0322	0.1906	0.093	0.5923	0.0349	-0.0728	0.0802	0.084	-0.0287	0.025	-0.1159	0.011	0.015	0.1813	-0.0611	0.0378	0.1501	-0.0515	0.1361	55.0504	40.1707	131.9741
2	0.3331	-0.072	0.1102	-0.0093	-0.0276	0.137	0.1005	-0.0478	-0.0561	0.0405	-0.0462	0.0008	0.0076	0.0292	0.0255	0.1001	-0.0262	0.0089	0.1333	-0.0128	0.1772	47.7225	11.6603	118.1579
3	0.2541	0.0722	-0.2382	0.5639	-0.0965	0.4339	0.0253	-0.0635	-0.0544	-0.0218	-0.0364	-0.0673	-0.0024	0.0424	-0.004	0.0805	-0.0328	0.0295	0.1228	-0.0187	0.1333	60.2441	19.081	117.9846
4	0.3199	-0.1926	-0.3412	0.4992	0.4004	0.9605	0.1298	0.0768	0.0323	-0.0474	0.0185	-0.011	-0.1561	-0.1194	0.1859	0.1161	0.0317	0.0261	0.1208	0.0352	0.1675	19.0813	19.8329	113.9613
5	0.413	-0.177	0.2163	0.0794	-0.1263	0.1632	0.1293	-0.1794	-0.0914	0.0957	-0.0187	0.0351	-0.05	0.0647	0.2182	0.2154	-0.0623	0.1066	0.2943	-0.0365	0.1089	38.3235	29.2805	147.0684
6	0.1396	0.0423	-0.0014	0.1744	0.2636	0.2726	0.1141	-0.0549	0.1901	0.0183	-0.1108	0.0196	0.0643	-0.0485	-0.0003	0.1834	0.0064	0.053	0.2234	0.0227	0.216	17.2458	21.8233	136.6445
7	0.351	-0.025	-0.2274	-0.0671	0.3092	0.5864	0.1271	-0.1188	-0.0515	0.0185	0.0038	0.0586	-0.0174	-0.046	0.0412	0.1761	-0.009	0.0444	0.1802	0.0272	0.1693	17.0718	22.6406	138.9897
8	0.1252	0.0012	0.1232	0.18	0.0114	0.0931	0.0762	-0.1808	0.0765	-0.0553	-0.0264	-0.2716	-0.0333	0.0643	0.001	0.2089	-0.0236	0.0837	0.2505	-0.0415	0.2212	24.5572	30.0461	140.4747
9	0.6079	0.2154	-0.4848	0.2413	-0.3433	0.5128	0.0166	0.1329	0.0929	0.0001	0.0218	0.0743	-0.1354	0.0522	-0	0.2339	0.0372	0.0013	0.2004	0.0137	0.1549	23.0749	42.2747	173.707
10	0.1568	0.0185	0.1333	0.1728	-0.2038	0.1191	0.0423	0.0094	-0.0876	0.0702	0.0108	0.0973	-0.0349	-0.0158	0.0007	0.193	0.0254	0.0148	0.1472	0.0025	0.1619	26.2317	20.9258	189.0446
11	0.3402	-0.1137	-0.2263	0.5242	-0.1044	0.3385	-0.0273	0.0676	-0.1575	0.0777	0.0083	0.2104	-0.0325	0.02	-0.011	0.192	0.0305	0.052	0.1706	-0.0024	0.2344	16.1806	20.0605	188.8357
12	0.4821	0.3076	-0.243	0.4315	-0.2179	0.3456	0.0729	-0.0586	-0.0559	0.0381	-0.0661	-0.1136	-0.0509	0.037	-0	0.2283	-0.0078	-0.0091	0.1823	-0.0018	0.1858	57.0739	17.99	193.7256
13	0.0458	-0.074	0.0039	0.0218	0.0673	0.0329	0.0321	0.2106	-0.0603	-0.1119	-0.0303	-0.0001	0.0251	-0.0283	-0.0004	0.2712	0.0099	0.0287	0.3284	-0.0301	0.1658	39.6166	28.2063	161.9702
14	-0.0037	-0.0311	0.04	0.0798	-0.1453	0.1391	-0.0718	0.1653	-0.0348	0.0328	-0.0834	-0.0281	-0.0205	0.3038	-0.0021	0.2903	0.0295	0.0291	0.2934	-0.0176	0.2115	63.2064	22.9837	172.8017
15	0.0833	0.0697	0.0222	0.0088	-0.0155	0.1802	0.0096	0.1332	-0.1816	-0.039	-0.0505	-0.0799	0.0755	0.0349	-0.0001	0.2785	0.0297	0.0501	0.2594	-0.0357	0.2069	58.2345	17.5462	168.1069
16	0.1089	-0.0318	0.122	0.0513	0.0391	0.0963	-0.0137	0.183	-0.1097	0.1143	-0.0924	0.0871	-0.0267	-0.0514	0.0014	0.2653	0.0376	0.0558	0.3044	-0.0318	0.1643	54.8325	29.9637	166.8919

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 135:293)
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 446:477)
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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Experimental details

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