PDB-5is9: Crystal structure of mouse CARM1 in complex with inhibitor SA0375

ID or keywords:

Entry

Database: PDB / ID: 5is9

Title

Crystal structure of mouse CARM1 in complex with inhibitor SA0375

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 / 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: 2.4 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 SA0375
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

-
Download

PDBx/mmCIF format	5is9.cif.gz	807.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5is9.ent.gz	691.8 KB	Display	PDB format
PDBx/mmJSON format	5is9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5is9_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	5is9_full_validation.pdf.gz	1.6 MB	Display
Data in XML	5is9_validation.xml.gz	55.5 KB	Display
Data in CIF	5is9_validation.cif.gz	76.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/is/5is9 ftp://data.pdbj.org/pub/pdb/validation_reports/is/5is9	HTTPS FTP

-
Related structure data

Related structure data	5ih3S S: Starting model for refinement
Similar structure data	5isg-d 5ise-d 6s70-d 4ikp-d 5tbh-d 6s7b-d 5k8v-d 5lv2-2 5ih3-d 5is6-d 5dx8-d 5k8x-d 6s71-d 5isd-d 5u4x-d 5isb-d 6arv-d 6s74-d 5ish-d 5lv3-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

-
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

168 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)	74.888, 98.374, 206.937
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-744- HOH

-
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

-
Non-polymers , 7 types, 539 molecules

#2: Chemical	ChemComp-6D3 / (2S)-2-amino-4-[(3-{4-[(2S)-2-amino-2-carboxyethyl]-1H-1,2,3-triazol-1-yl}propyl){[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}amino]butanoic acid (non-preferred name) Mass: 563.567 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₂H₃₃N₁₁O₇
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-DXE / 1,2-DIMETHOXYETHANE Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#6: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#7: Chemical	ChemComp-M2M / 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.27 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop Details: Tris-HCl pH 8.0 100 mM PEG 2000 MME 13 % NaCl 100 mM

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.4→20 Å / Num. obs: 64352 / % possible obs: 99.7 % / Redundancy: 4.4 % / B_iso Wilson estimate: 32.36 Å² / R_sym value: 0.091 / Net I/σ(I): 16.8
Reflection shell	Resolution: 2.4→2.49 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.6 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
PHENIX	(dev_2016: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3

Resolution: 2.4→19.601 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.91

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2057	3191	4.96 %	Random selection
R_work	0.1676	-	-	-
obs	0.1695	64296	95.77 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.4→19.601 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11004	0	286	511	11801

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	11731
X-RAY DIFFRACTION	f_angle_d	0.974	15872
X-RAY DIFFRACTION	f_dihedral_angle_d	14.486	4213
X-RAY DIFFRACTION	f_chiral_restr	0.041	1720
X-RAY DIFFRACTION	f_plane_restr	0.004	2016

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 (%)
2.3179-2.3524	0.254	24	0.1903	608	X-RAY DIFFRACTION	22
2.3524-2.3891	0.2627	111	0.2015	2429	X-RAY DIFFRACTION	87
2.3891-2.4282	0.2531	163	0.1997	2705	X-RAY DIFFRACTION	100
2.4282-2.47	0.2411	146	0.2012	2711	X-RAY DIFFRACTION	100
2.47-2.5148	0.2582	128	0.1919	2721	X-RAY DIFFRACTION	99
2.5148-2.5631	0.242	152	0.1934	2730	X-RAY DIFFRACTION	100
2.5631-2.6153	0.2504	133	0.1962	2721	X-RAY DIFFRACTION	100
2.6153-2.672	0.2362	153	0.1943	2763	X-RAY DIFFRACTION	100
2.672-2.734	0.2676	131	0.1876	2728	X-RAY DIFFRACTION	100
2.734-2.8022	0.2335	145	0.1883	2751	X-RAY DIFFRACTION	100
2.8022-2.8777	0.2403	140	0.1814	2755	X-RAY DIFFRACTION	100
2.8777-2.9621	0.2218	126	0.1899	2728	X-RAY DIFFRACTION	100
2.9621-3.0574	0.2042	154	0.1868	2740	X-RAY DIFFRACTION	100
3.0574-3.1662	0.2202	152	0.1882	2748	X-RAY DIFFRACTION	100
3.1662-3.2924	0.2348	144	0.1899	2766	X-RAY DIFFRACTION	100
3.2924-3.4415	0.1994	133	0.1724	2788	X-RAY DIFFRACTION	100
3.4415-3.6219	0.2247	130	0.1627	2766	X-RAY DIFFRACTION	100
3.6219-3.8472	0.194	155	0.1539	2756	X-RAY DIFFRACTION	100
3.8472-4.1417	0.177	165	0.1376	2791	X-RAY DIFFRACTION	99
4.1417-4.5537	0.156	146	0.1235	2782	X-RAY DIFFRACTION	100
4.5537-5.2019	0.1657	129	0.1254	2838	X-RAY DIFFRACTION	100
5.2019-6.5136	0.1817	160	0.1701	2843	X-RAY DIFFRACTION	100
6.5136-19.6016	0.1889	171	0.1805	2937	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	1.0994	-0.4123	0.0873	0.89	0.0595	1.0632	0.0259	-0.1326	0.1636	0.1391	-0.0505	0.0424	-0.1462	-0.0016	0.0013	0.2705	-0.0807	0.0478	0.2182	-0.073	0.2544	55.1505	40.2041	133.3413
2	0.6273	0.1381	0.4514	-0.0152	0.0642	0.3454	0.116	-0.0666	-0.0487	0.0034	-0.0416	-0.0141	-0.0049	0.0566	0.0115	0.1565	-0.0392	0.0364	0.1644	-0.0234	0.2659	48.1076	12.1823	119.2003
3	0.9679	0.1421	-0.102	1.5223	0.0409	1.149	0.0047	-0.0002	-0.0357	-0.0795	-0.0252	-0.1004	0.0329	0.0353	0.0004	0.147	-0.0551	0.051	0.1773	-0.0191	0.2098	60.3413	19.1797	119.2765
4	0.9493	-0.3565	-0.3579	0.8986	0.565	1.7	0.135	0.074	0.0105	-0.0593	0.0301	0.016	-0.1929	-0.1552	0.0095	0.1909	0.0513	0.0406	0.1553	0.0547	0.2565	18.8887	19.7008	115.0595
5	0.3906	0.2402	0.1554	-0.0864	-0.0992	0.1969	0.1748	-0.2034	-0.3201	0.0651	0.0115	-0.0766	-0.0714	0.021	0.0007	0.3389	-0.0389	0.0698	0.3999	-0.0155	0.3298	38.3043	29.1667	148.2688
6	0.4323	0.1863	0.018	0.4587	0.6404	0.658	-0.006	-0.1471	-0.0009	0.0835	-0.0215	0.0758	-0.0076	-0.2801	0.0006	0.23	0.0129	0.0879	0.2966	0.0487	0.327	17.1444	21.8838	137.7348
7	0.722	-0.0554	-0.4973	0.4562	0.1818	1.1594	0.0923	-0.1706	-0.0247	0.0964	-0.0151	0.0006	-0.1008	-0.0108	0.0006	0.2238	0.0181	0.0389	0.2737	0.064	0.2471	16.9099	22.5677	140.319
8	0.5623	0.3978	0.5907	0.3311	0.2644	0.598	0.0701	-0.3036	-0.0428	0.0113	0.0551	-0.2417	-0.0209	0.0671	0.0001	0.3527	0.0402	0.0945	0.385	0.0281	0.3977	25.5731	28.6197	141.0076
9	1.3125	0.5363	-0.94	0.3426	-0.3844	1.1236	0.0995	0.1811	0.277	0.0784	0.0885	0.0673	-0.2294	0.0047	0.0005	0.4675	0.0826	0.0752	0.4414	0.0437	0.3955	23.1071	42.2036	175.263
10	0.5606	-0.0846	0.1826	0.1885	-0.1764	0.0955	0.082	0.0015	-0.1193	0.0155	0.0124	0.0975	-0.0389	-0.0623	-0	0.3557	0.0438	0.0287	0.3204	0.0073	0.2778	26.1347	20.8432	190.7915
11	1.0948	-0.3914	-0.6884	1.0394	-0.3135	0.9792	-0.0164	0.0553	-0.172	0.0628	-0.0417	0.2202	0.0508	-0.1012	-0.0002	0.3376	0.0528	0.0583	0.4025	-0.0231	0.3277	16.3386	20.1765	190.6446
12	0.4988	0.3114	-0.1918	1.2052	-0.3034	1.0591	0.1431	-0.1085	-0.0238	0.0674	-0.1	-0.0697	-0.1096	0.163	0.0001	0.3176	-0.0323	0.0054	0.3319	-0.0408	0.2763	57.4201	17.9825	195.6172
13	0.4297	-0.7092	0.0284	0.067	0.0173	0.2975	0.1602	0.3264	-0.1649	-0.0882	-0.1141	0.0839	0.0279	-0.1269	-0.0001	0.39	-0.0039	0.06	0.5418	-0.0523	0.3506	39.9467	28.234	163.7761
14	0.3201	-0.0524	-0.0897	0.3144	-0.4143	0.5859	-0.2007	0.1936	-0.1443	-0.0253	0.1154	-0.0793	-0.1148	0.7063	-0.0288	0.4073	0.0037	0.0453	0.5029	-0.029	0.3418	63.7515	23.3634	175.3346
15	0.6714	0.416	0.0763	0.296	-0.0946	0.3204	-0.0917	0.087	-0.1296	-0.0759	-0.0508	-0.1105	0.1657	0.0312	-0	0.3978	0.0048	0.0664	0.4039	-0.0514	0.3146	58.3171	17.5207	170.198
16	0.4525	-0.239	0.5086	0.2908	-0.0189	0.5449	0.0318	0.1233	-0.1152	0.0542	-0.0952	0.2234	-0.1308	-0.114	-0.0006	0.4254	0.0046	0.0627	0.445	-0.058	0.3504	53.584	28.709	169.2746

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)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 7 types, 539 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 7 types, 539 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 7 types, 539 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi