PDB-5k8x: Crystal structure of mouse CARM1 in complex with inhibitor U3

ID or keywords:

Entry

Database: PDB / ID: 5k8x

Title

Crystal structure of mouse CARM1 in complex with inhibitor U3

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 / type I protein arginine methyltransferase / Cytoprotection by HMOX1 ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.991 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 U3
Authors: Cura, V. / Marechal, N. / Mailliot, J. / Troffer-Charlier, N. / Wurtz, J.M. / Bonnefond, L. / Cavarelli, J.

History

Deposition	May 31, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 21, 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

-
Download

PDBx/mmCIF format	5k8x.cif.gz	814.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5k8x.ent.gz	696.2 KB	Display	PDB format
PDBx/mmJSON format	5k8x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k8/5k8x ftp://data.pdbj.org/pub/pdb/validation_reports/k8/5k8x	HTTPS FTP

-
Related structure data

Related structure data	5ih3S S: Starting model for refinement
Similar structure data	5tbj-d 5lv2-1 6s71-d 6s79-d 2y1w-d 5isa-d 5k8v-d 5tbh-d 5isg-d 5tbi-d 5is7-d 5ish-d 6s7c-d 5dwq-d 5lv2-2 5lv3-d 5is6-d 6s7a-d 5u4x-d 5ntc-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

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)	74.831, 98.486, 205.530
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

-
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 , 8 types, 866 molecules

#2: Chemical	ChemComp-6ZH / [[[(~{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]amino]-azanyl-methylidene]azanium Mass: 335.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₃H₁₉N₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Chemical	ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Polyethylene glycol Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₉
#7: Chemical	ChemComp-DXE / 1,2-DIMETHOXYETHANE / Dimethoxyethane Mass: 90.121 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#8: Chemical	ChemComp-M2M / 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE / Diglyme Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₃
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 834 / 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: 2.32 Å³/Da / Density % sol: 46.92 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris-HCl pH 8.0 100 mM, PEG 2000 MME 15 %, NaCl 100 mM

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.99→49.24 Å / Num. obs: 103982 / % possible obs: 99.2 % / Redundancy: 6.6 % / B_iso Wilson estimate: 29.19 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.161 / Net I/σ(I): 7.3
Reflection shell	Resolution: 1.99→2.01 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 0.8 / % possible all: 84.8

-
Processing

Software

Name	Version	Classification
PHENIX	dev_1980	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3

Resolution: 1.991→45.555 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.45

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2115	5174	4.98 %	Random selection
R_work	0.1699	-	-	-
obs	0.172	103907	99.19 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.991→45.555 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10993	0	270	834	12097

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11653
X-RAY DIFFRACTION	f_angle_d	1.002	15732
X-RAY DIFFRACTION	f_dihedral_angle_d	14.948	4287
X-RAY DIFFRACTION	f_chiral_restr	0.047	1701
X-RAY DIFFRACTION	f_plane_restr	0.004	2060

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 (%)
1.9908-2.0135	0.3717	131	0.3547	2516	X-RAY DIFFRACTION	77
2.0135-2.0372	0.2983	197	0.2978	3256	X-RAY DIFFRACTION	100
2.0372-2.062	0.3049	192	0.2863	3267	X-RAY DIFFRACTION	100
2.062-2.0881	0.3091	145	0.2692	3301	X-RAY DIFFRACTION	100
2.0881-2.1156	0.3175	160	0.2608	3265	X-RAY DIFFRACTION	100
2.1156-2.1446	0.288	179	0.2485	3303	X-RAY DIFFRACTION	100
2.1446-2.1752	0.298	164	0.2365	3271	X-RAY DIFFRACTION	100
2.1752-2.2077	0.2757	190	0.226	3277	X-RAY DIFFRACTION	100
2.2077-2.2422	0.2883	183	0.22	3283	X-RAY DIFFRACTION	100
2.2422-2.2789	0.259	169	0.2096	3269	X-RAY DIFFRACTION	100
2.2789-2.3182	0.2318	165	0.2	3265	X-RAY DIFFRACTION	100
2.3182-2.3604	0.2543	144	0.1944	3325	X-RAY DIFFRACTION	100
2.3604-2.4058	0.2338	182	0.1846	3293	X-RAY DIFFRACTION	100
2.4058-2.4549	0.2107	175	0.1809	3301	X-RAY DIFFRACTION	100
2.4549-2.5082	0.2527	165	0.1812	3283	X-RAY DIFFRACTION	100
2.5082-2.5666	0.2401	176	0.1737	3303	X-RAY DIFFRACTION	100
2.5666-2.6308	0.2084	169	0.1715	3307	X-RAY DIFFRACTION	100
2.6308-2.7019	0.2049	180	0.1662	3304	X-RAY DIFFRACTION	100
2.7019-2.7814	0.2524	158	0.171	3318	X-RAY DIFFRACTION	100
2.7814-2.8711	0.2173	166	0.1741	3322	X-RAY DIFFRACTION	100
2.8711-2.9737	0.2185	165	0.1711	3304	X-RAY DIFFRACTION	100
2.9737-3.0928	0.24	187	0.1693	3325	X-RAY DIFFRACTION	100
3.0928-3.2335	0.2251	172	0.1617	3308	X-RAY DIFFRACTION	100
3.2335-3.4039	0.1927	171	0.1643	3350	X-RAY DIFFRACTION	100
3.4039-3.6171	0.2116	153	0.1459	3342	X-RAY DIFFRACTION	100
3.6171-3.8962	0.1744	197	0.131	3348	X-RAY DIFFRACTION	100
3.8962-4.2881	0.1532	187	0.1178	3355	X-RAY DIFFRACTION	100
4.2881-4.9079	0.1384	163	0.1083	3391	X-RAY DIFFRACTION	100
4.9079-6.181	0.17	180	0.1429	3444	X-RAY DIFFRACTION	100
6.181-45.5671	0.1953	209	0.186	3537	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	0.8955	0.0279	-0.0608	0.4238	0.0518	1.2811	0.0237	-0.1346	0.148	0.0977	-0.0482	0.0363	-0.1065	-0.0069	0.0002	0.2418	-0.042	0.0174	0.2222	-0.051	0.2223	55.2568	40.4931	132.3367
2	0.5765	0.2103	0.2887	-0.1747	-0.0467	0.1987	0.117	-0.0376	0.0599	0.045	-0.0624	0.0814	0.0405	0.0427	0.006	0.1434	-0.0077	0.0072	0.1724	-0.0177	0.2512	47.8068	11.8278	118.4929
3	0.7411	0.2459	-0.2173	1.5263	-0.1443	0.9209	-0.0587	-0.0353	-0.0297	-0.0869	0.0124	-0.0374	0.0561	-0.0273	-0.0432	0.1428	-0.0361	0.0498	0.1747	-0.0203	0.1962	60.4345	19.3082	118.4218
4	0.7446	-0.5876	-0.3546	1.427	0.4344	1.6112	0.0923	0.0857	0.0016	-0.0271	0.0423	-0.0198	-0.0991	-0.1351	0.0023	0.1579	0.0324	0.0172	0.1796	0.0225	0.2159	19.0229	19.9711	114.4083
5	0.5906	0.4965	0.5145	-0.3584	-0.0899	0.0537	0.3448	-0.248	-0.0941	0.2602	-0.2051	0.0034	0.0733	0.0448	0.0077	0.3472	-0.0787	0.0447	0.4319	-0.0223	0.2717	38.5347	29.4787	147.6778
6	0.387	-0.1162	-0.022	0.6095	0.6261	0.545	0.0756	-0.2332	0.1735	0.0385	-0.1181	-0.0757	0.2042	-0.1132	-0	0.2587	-0.0161	0.0483	0.3274	0.0226	0.3123	17.2125	21.9305	137.2003
7	0.9308	-0.2541	-0.0301	0.0586	0.1867	0.8235	0.0914	-0.2475	0.0179	0.1127	-0.0119	0.0266	-0.028	-0.0452	-0	0.3021	-0.0298	0.0146	0.3151	0.0367	0.2468	17.0292	22.7	139.4723
8	0.3353	0.0532	0.3555	0.4656	0.0943	0.3474	0.0602	-0.3516	0.1001	0.0736	0.012	-0.2309	0.292	0.1684	0.0007	0.296	-0.0153	0.0664	0.3641	-0.0582	0.3362	24.6424	30.0649	140.9225
9	1.1669	-0.0033	-0.5469	0.6902	-0.27	1.4215	-0.0052	0.1411	0.0859	0.0466	0.0139	0.0577	-0.1028	0.0385	0	0.314	0.0478	0.0129	0.2966	0.0209	0.2481	23.124	42.5582	174.2927
10	0.6011	-0.1038	0.3589	0.3374	-0.4606	0.1512	0.0613	0.0532	-0.1897	0.1172	-0.0084	0.1824	-0.0357	-0.0368	-0	0.2931	0.0381	0.0181	0.2381	-0.0007	0.245	26.1685	21.1156	189.4741
11	0.6267	-0.4484	-0.126	1.156	-0.234	0.7163	-0.0379	0.0719	-0.1727	0.1311	0.0242	0.2958	0.0205	0.0011	-0.0287	0.2938	0.035	0.0773	0.2627	0.001	0.3464	16.0657	20.2909	189.4784
12	0.8881	0.7372	-0.5944	1.5606	-0.3968	1.1518	0.082	-0.1266	-0.0963	0.0552	-0.1169	-0.1655	-0.0263	0.0436	-0	0.2919	-0.0145	-0.0303	0.2426	0.0046	0.2644	57.2952	18.1605	194.0845
13	0.5262	-0.8152	0.3873	-0.2402	0.1004	-0.2427	0.2564	0.3111	-0.1849	-0.2933	-0.179	0.0757	0.1202	-0.0567	0.0003	0.3892	0.0683	0.0489	0.4076	-0.0227	0.2954	39.6862	28.3893	162.4035
14	0.463	-0.0912	-0.1169	0.209	-0.2752	0.373	-0.0164	0.1373	-0.0279	-0.0556	-0.1166	-0.0859	-0.029	0.1459	-0.0001	0.351	0.014	0.0241	0.373	-0.0018	0.3453	63.4648	23.2277	173.1344
15	0.189	0.1302	0.1801	0.0784	0.1571	0.349	0.0359	0.2313	-0.1594	-0.0677	-0.0777	-0.0767	0.0349	0.2428	-0	0.3865	0.0446	0.0422	0.3465	-0.0438	0.2742	58.4917	17.6772	168.4658
16	0.4628	-0.1303	0.3909	0.4018	0.1899	0.3712	0.008	0.1889	-0.1433	0.0668	-0.1507	0.0906	-0.0965	-0.0447	-0.0003	0.3205	0.0368	0.0351	0.3758	-0.0274	0.2418	54.7707	30.1739	167.2991

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)

-
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 , 8 types, 866 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 , 8 types, 866 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 , 8 types, 866 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