PDB-5is6: Crystal structure of mouse CARM1 in complex with Sinefungin at 2....

ID or keywords:

Entry

Database: PDB / ID: 5is6

Title

Crystal structure of mouse CARM1 in complex with Sinefungin at 2.0 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

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

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.007 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 Sinefungin at 2.0 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 2.0	Jan 10, 2024	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5is6.cif.gz	812.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5is6.ent.gz	688.7 KB	Display	PDB format
PDBx/mmJSON format	5is6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5is6_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	5is6_full_validation.pdf.gz	1.5 MB	Display
Data in XML	5is6_validation.xml.gz	60.5 KB	Display
Data in CIF	5is6_validation.cif.gz	88.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/is/5is6 ftp://data.pdbj.org/pub/pdb/validation_reports/is/5is6	HTTPS FTP

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Related structure data

Related structure data	5ih3S S: Starting model for refinement
Similar structure data	5lv3-d 6s77-d 5lv2-1 5tbi-d 6s70-d 6s71-d 2y1x-d 6s7b-d 5tbh-d 5dx8-d 2y1w-d 6s79-d 5isg-d 5k8v-d 5dxa-d 6s7a-d 5lv2-2 6s7c-d 5dwq-d 5k8x-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) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #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 software

Unit cell

Length a, b, c (Å)	74.685, 98.090, 206.369
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	A-820- HOH
2	1	C-814- HOH
3	1	C-862- 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 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 , 6 types, 1060 molecules

#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-DXE / 1,2-DIMETHOXYETHANE Mass: 90.121 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#6: Chemical	ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE Mass: 381.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₇O₅
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1036 / 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: 2.31 Å³/Da / Density % sol: 46.82 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris-HCl pH 8.0 100 mM PEG 2000 MME 28 % NaCl 100 mM

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9724 Å / Relative weight: 1
Reflection	Resolution: 2→20.2 Å / Num. obs: 100193 / % possible obs: 99.8 % / Redundancy: 6.2 % / R_sym value: 0.076 / Net I/σ(I): 22.7
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 5.3 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2313: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3

Resolution: 2.007→20.167 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 16.41

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1772	4976	4.97 %	Random selection
R_work	0.1373	-	-	-
obs	0.1393	100125	98.25 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.007→20.167 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11000	0	236	1036	12272

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	11573
X-RAY DIFFRACTION	f_angle_d	1.095	15640
X-RAY DIFFRACTION	f_dihedral_angle_d	15.198	6845
X-RAY DIFFRACTION	f_chiral_restr	0.116	1704
X-RAY DIFFRACTION	f_plane_restr	0.008	2036

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 (%)
2.0073-2.0301	0.2316	95	0.1637	1652	X-RAY DIFFRACTION	53
2.0301-2.054	0.2158	187	0.1553	3170	X-RAY DIFFRACTION	99
2.054-2.079	0.1825	145	0.1507	3201	X-RAY DIFFRACTION	100
2.079-2.1053	0.1864	157	0.1493	3172	X-RAY DIFFRACTION	100
2.1053-2.133	0.2241	161	0.1472	3238	X-RAY DIFFRACTION	100
2.133-2.1622	0.2016	173	0.1413	3148	X-RAY DIFFRACTION	100
2.1622-2.193	0.1946	170	0.1377	3178	X-RAY DIFFRACTION	100
2.193-2.2257	0.1885	190	0.1261	3162	X-RAY DIFFRACTION	100
2.2257-2.2604	0.1797	161	0.1311	3198	X-RAY DIFFRACTION	100
2.2604-2.2975	0.1628	153	0.126	3180	X-RAY DIFFRACTION	100
2.2975-2.337	0.1747	163	0.1305	3241	X-RAY DIFFRACTION	100
2.337-2.3794	0.2072	147	0.1259	3178	X-RAY DIFFRACTION	100
2.3794-2.4251	0.1744	183	0.13	3180	X-RAY DIFFRACTION	100
2.4251-2.4746	0.1886	173	0.1308	3204	X-RAY DIFFRACTION	100
2.4746-2.5283	0.1918	152	0.1267	3205	X-RAY DIFFRACTION	100
2.5283-2.587	0.1813	177	0.1282	3206	X-RAY DIFFRACTION	100
2.587-2.6515	0.1698	165	0.1281	3199	X-RAY DIFFRACTION	100
2.6515-2.723	0.1792	162	0.1299	3221	X-RAY DIFFRACTION	100
2.723-2.803	0.1747	168	0.1357	3216	X-RAY DIFFRACTION	100
2.803-2.8932	0.177	167	0.1397	3214	X-RAY DIFFRACTION	100
2.8932-2.9963	0.1958	154	0.1468	3255	X-RAY DIFFRACTION	100
2.9963-3.1158	0.1993	190	0.1535	3179	X-RAY DIFFRACTION	100
3.1158-3.2571	0.184	159	0.1508	3252	X-RAY DIFFRACTION	100
3.2571-3.428	0.1625	160	0.1477	3261	X-RAY DIFFRACTION	100
3.428-3.6416	0.1831	158	0.1377	3265	X-RAY DIFFRACTION	100
3.6416-3.9209	0.1636	189	0.1312	3248	X-RAY DIFFRACTION	100
3.9209-4.312	0.1474	180	0.1174	3251	X-RAY DIFFRACTION	100
4.312-4.928	0.1409	159	0.1105	3318	X-RAY DIFFRACTION	100
4.928-6.1789	0.1686	176	0.1446	3344	X-RAY DIFFRACTION	100
6.1789-20.1677	0.1876	202	0.1743	3413	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	0.6043	-0.2713	-0.0842	0.5636	-0.0108	0.8584	0.0307	-0.1008	0.1048	0.0707	-0.0156	0.0365	-0.1268	0.0309	0.0426	0.1492	-0.051	0.0293	0.1487	-0.0558	0.1266	55.1487	40.1383	132.9315
2	0.5307	0.0504	0.231	-0.0571	0.1613	0.3151	0.106	-0.0333	-0.0947	0.0284	-0.0427	0.0148	0.0385	0.0317	0.0167	0.1262	-0.026	0.0105	0.1332	-0.0075	0.1948	47.875	11.8288	118.9404
3	0.1726	-0.0155	-0.1469	1.0422	0.1497	0.7236	0.0311	-0.0388	-0.0367	-0.0643	-0.0081	-0.0592	0.0419	0.0363	0.0155	0.1003	-0.0281	0.0306	0.1522	-0.0163	0.1538	60.3529	19.0269	118.8792
4	0.4623	-0.1862	-0.3946	0.8221	0.5615	1.3008	0.1054	0.0762	0.0312	-0.0517	0.0145	-0.0185	-0.1475	-0.105	0.079	0.1366	0.0248	0.0205	0.1241	0.0215	0.16	19.0637	19.7309	114.7093
5	0.538	0.2147	0.1707	0.141	-0.0879	0.1614	0.1857	-0.2466	-0.2134	0.1548	-0.0894	-0.0651	0.0773	0.056	0.054	0.2401	-0.0596	0.0747	0.287	-0.0325	0.173	38.4684	29.2061	148.0371
6	0.1256	0.0032	0.0058	0.2992	0.3575	0.4066	0.1038	-0.0597	0.155	0.1062	-0.1256	0.0207	0.0907	-0.0653	0	0.1992	-0.0097	0.0473	0.2388	0.0045	0.2357	17.3093	21.7849	137.3837
7	0.4681	-0.0284	-0.1163	0.0592	0.2788	0.9017	0.1306	-0.1045	-0.016	0.052	-0.0455	-0.0192	0.0111	-0.0266	0.0462	0.1899	-0.0233	0.0418	0.1945	0.0162	0.1727	17.1462	22.6435	139.8095
8	0.216	0.0509	0.2214	0.3407	0.0038	0.2175	0.1303	-0.2351	0.046	-0.0323	-0.0443	-0.2125	-0.031	0.1761	0.0025	0.2276	-0.0243	0.0697	0.2502	-0.0227	0.2296	24.9676	29.7215	141.2328
9	0.8041	0.2287	-0.7023	0.4416	-0.1001	0.8401	0.06	0.131	0.1305	-0.0276	0.0074	0.0422	-0.1471	0.0472	0.0001	0.2143	0.0158	0.0186	0.1941	0.0227	0.1699	23.0432	42.312	174.8433
10	0.491	-0.0318	0.2768	0.1611	-0.2238	0.1738	0.0413	-0.0049	-0.1238	0.0343	0.0076	0.1234	-0.0251	-0.0092	0	0.1809	0.0162	0.0214	0.1543	0.0023	0.1691	26.045	21.1522	190.2036
11	0.5338	-0.311	-0.1797	0.6196	-0.2047	0.3065	-0.0146	0.0365	-0.1476	0.0533	0.0098	0.1904	0.0131	-0.011	-0.0051	0.1778	0.0149	0.0306	0.1701	-0.0103	0.2301	16.5411	20.2185	190.0886
12	0.6234	0.3687	-0.2205	0.6918	-0.1427	0.6781	0.0559	-0.0683	-0.0315	0.0297	-0.0339	-0.0655	-0.0599	0.0411	-0	0.1757	-0.0003	0.0022	0.1432	-0.0131	0.1786	57.1924	18.0066	195.1198
13	0.3011	-0.159	0.0342	0.075	0.0332	0.0749	0.1131	0.2052	-0.1101	-0.1194	-0.0684	0.0282	0.0275	-0.0261	-0	0.23	0.014	0.028	0.2975	-0.0171	0.1729	39.6677	28.1331	163.2019
14	0.1149	-0.0671	-0.008	0.1524	-0.2094	0.3634	-0.0695	0.1436	0.0323	0.017	-0.0748	-0.0177	-0.0439	0.2833	-0.0162	0.2367	0.0336	0.0318	0.2498	-0.0209	0.218	63.2176	22.9758	174.0533
15	0.2411	0.1439	-0.1115	0.1222	-0.1988	0.2411	0.0252	0.1404	-0.1226	-0.0842	-0.0288	-0.0569	0.161	0.058	0	0.2339	0.0264	0.0276	0.2214	-0.0361	0.1946	58.2536	17.4987	169.3916
16	0.2002	-0.0454	0.2285	0.2105	0.0372	0.2717	0.0793	0.1732	-0.0986	0.0938	-0.0978	0.0498	-0.135	-0.0688	0.0005	0.2229	0.0364	0.034	0.2825	-0.0263	0.1835	54.8665	29.9839	168.0611

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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