PDB-5k8v: Crystal Structure of Mus musculus Protein Arginine Methyltransfer...

ID or keywords:

Entry

Database: PDB / ID: 5k8v

Title

Crystal Structure of Mus musculus Protein Arginine Methyltransferase 4 (CARM1 130-487) with CP1

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: 2.25 Å

Authors

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

Citation

Journal: FEBS J. / Year: 2017
Title: Structural studies of protein arginine methyltransferase 2 reveal its interactions with potential substrates and inhibitors.
Authors: Cura, V. / Marechal, N. / Troffer-Charlier, N. / Strub, J.M. / van Haren, M.J. / Martin, N.I. / Cianferani, S. / Bonnefond, L. / Cavarelli, J.

History

Deposition	May 31, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 30, 2016	Group: Database references
Revision 1.2	Dec 7, 2016	Group: Database references
Revision 1.3	Jan 18, 2017	Group: Database references
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	5k8v.cif.gz	799.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5k8v.ent.gz	681.7 KB	Display	PDB format
PDBx/mmJSON format	5k8v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k8/5k8v ftp://data.pdbj.org/pub/pdb/validation_reports/k8/5k8v	HTTPS FTP

-
Related structure data

Related structure data	5fubC 5fulC 5fwaC 5fwdC 5g02C 5jmqC 5ih3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6s7c-d 2y1w-d 5ish-d 5k8x-d 5lv3-d 5lv2-2 5tbj-d 6s77-d 5is6-d 5lv2-1 6s70-d 6s79-d 5isg-d 5tbi-d 5is9-d 5tbh-d 5isd-d 6s7a-d 6s71-d 5isa-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) #222 - Jun 2018 Proteins and Nanoparticles 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

166 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)	75.084, 98.094, 206.260
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-732- HOH
2	1	A-762- HOH
3	1	A-763- 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 , 6 types, 614 molecules

#2: Chemical	ChemComp-6RE / [[2-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethylamino]-azanyl-methylidene]azanium Mass: 323.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₈O₃
#3: Chemical	ChemComp-DXE / 1,2-DIMETHOXYETHANE / Dimethoxyethane Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₆
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 596 / 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: 47.08 %
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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9801 Å / Relative weight: 1
Reflection	Resolution: 2.25→47.72 Å / Num. obs: 73068 / % possible obs: 99.8 % / Redundancy: 6.5 % / B_iso Wilson estimate: 29.61 Å² / CC_1/2: 0.986 / R_merge(I) obs: 0.282 / Net I/σ(I): 5.7
Reflection shell	Resolution: 2.25→2.3 Å / Redundancy: 6.6 % / R_merge(I) obs: 2.132 / Mean I/σ(I) obs: 1.1 / % possible all: 97.6

-
Processing

Software

Name	Version	Classification
PHENIX	(dev_2386: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3

Resolution: 2.25→47.716 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2348	3600	4.93 %	Random selection
R_work	0.1924	-	-	-
obs	0.1945	72983	99.75 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.25→47.716 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10989	0	170	596	11755

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	11432
X-RAY DIFFRACTION	f_angle_d	0.477	15462
X-RAY DIFFRACTION	f_dihedral_angle_d	15.37	6762
X-RAY DIFFRACTION	f_chiral_restr	0.043	1688
X-RAY DIFFRACTION	f_plane_restr	0.003	2022

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 (%)
2.2501-2.2797	0.322	133	0.3002	2577	X-RAY DIFFRACTION	97
2.2797-2.3109	0.323	120	0.2948	2607	X-RAY DIFFRACTION	100
2.3109-2.3439	0.2986	128	0.2831	2672	X-RAY DIFFRACTION	100
2.3439-2.3789	0.3288	132	0.2758	2650	X-RAY DIFFRACTION	100
2.3789-2.4161	0.3129	147	0.2743	2614	X-RAY DIFFRACTION	100
2.4161-2.4557	0.3193	143	0.266	2650	X-RAY DIFFRACTION	100
2.4557-2.498	0.304	129	0.2594	2646	X-RAY DIFFRACTION	100
2.498-2.5434	0.281	136	0.2468	2608	X-RAY DIFFRACTION	100
2.5434-2.5924	0.285	136	0.253	2681	X-RAY DIFFRACTION	100
2.5924-2.6453	0.2897	140	0.2393	2644	X-RAY DIFFRACTION	100
2.6453-2.7028	0.2728	147	0.2273	2631	X-RAY DIFFRACTION	100
2.7028-2.7656	0.2719	117	0.2166	2666	X-RAY DIFFRACTION	100
2.7656-2.8348	0.292	143	0.2233	2630	X-RAY DIFFRACTION	100
2.8348-2.9114	0.28	140	0.2108	2672	X-RAY DIFFRACTION	100
2.9114-2.9971	0.2409	123	0.2082	2699	X-RAY DIFFRACTION	100
2.9971-3.0938	0.251	155	0.2029	2639	X-RAY DIFFRACTION	100
3.0938-3.2044	0.2626	141	0.1972	2636	X-RAY DIFFRACTION	100
3.2044-3.3326	0.2216	133	0.1873	2690	X-RAY DIFFRACTION	100
3.3326-3.4843	0.2286	124	0.1779	2673	X-RAY DIFFRACTION	100
3.4843-3.6679	0.2155	138	0.1594	2688	X-RAY DIFFRACTION	100
3.6679-3.8976	0.211	157	0.1543	2671	X-RAY DIFFRACTION	100
3.8976-4.1984	0.1745	146	0.1374	2689	X-RAY DIFFRACTION	100
4.1984-4.6206	0.1592	138	0.1267	2705	X-RAY DIFFRACTION	100
4.6206-5.2884	0.1771	134	0.1296	2735	X-RAY DIFFRACTION	100
5.2884-6.66	0.1981	152	0.1785	2753	X-RAY DIFFRACTION	100
6.66-47.727	0.2198	168	0.1966	2857	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	1.4886	-0.3393	-0.0762	1.2357	-0.0453	2.1876	0.0358	-0.2083	0.1701	0.0945	-0.0286	0.0153	-0.1297	-0.0196	0.0003	0.2721	-0.0573	0.0252	0.2457	-0.072	0.2599	55.4521	40.3119	132.8532
2	1.1105	0.3285	0.3688	0.0051	0.1736	0.2866	0.1175	-0.0481	-0.0751	0.0888	-0.0526	0.0496	0.0202	0.0821	0	0.2136	-0.0077	0.0206	0.198	0.0026	0.2948	48.1132	11.8896	118.9685
3	0.6915	0.249	-0.124	1.9117	0.3921	1.2165	0.0171	-0.1102	-0.1049	-0.0527	-0.0063	-0.0402	0.0522	0.0056	-0	0.1749	-0.0188	0.0338	0.2416	-0.0021	0.2346	60.6388	19.225	118.8578
4	1.0208	-0.4313	-0.7913	1.1581	0.5346	2.212	0.0723	0.0719	0.0631	-0.0169	0.0464	-0.009	-0.2118	-0.0996	0.0088	0.2109	0.0338	0.0151	0.1636	0.0175	0.2487	19.1517	19.9093	114.6272
5	0.8299	0.4002	0.2103	0.1038	0.0922	0.0449	0.346	-0.3109	-0.0994	0.1729	-0.2072	-0.0432	0.1305	0.1578	-0.0029	0.3924	-0.0595	0.0307	0.5012	-0.0034	0.2866	38.6514	29.4072	148.1567
6	0.9305	0.169	-0.1133	1.1013	1.1412	1.2296	0.1182	-0.2152	0.1809	0.1014	-0.1028	-0.1295	0.1649	-0.0563	0.0001	0.2524	0.0066	0.0729	0.3003	0.0096	0.3373	17.3278	21.8271	137.5508
7	1.6011	0.1238	0.1534	0.5807	0.4281	1.7811	0.1716	-0.3392	-0.0233	0.1455	-0.0642	-0.0411	-0.0312	-0.0428	0	0.2814	-0.0034	0.0126	0.2742	0.04	0.2465	17.1453	22.5747	139.8878
8	0.7995	0.1053	0.8032	0.4858	-0.0391	0.8199	0.0454	-0.3263	-0.0904	0.016	-0.0177	-0.3214	0.0109	0.4623	-0	0.3713	-0.0282	0.059	0.4287	-0.0539	0.4345	24.7572	30.0571	141.4884
9	1.8744	0.0902	-0.3964	1.1858	-0.4074	1.6645	0.0227	0.0817	0.0733	-0.0257	0.0227	0.0279	-0.1169	0.0185	0	0.3749	0.0395	0.0013	0.3182	0.0028	0.2603	23.2224	42.3958	174.8688
10	0.6036	-0.0203	0.2829	0.4483	-0.2436	0.2178	0.038	0.0641	-0.2113	0.018	0.0355	0.2532	-0.0443	-0.0433	-0	0.2942	0.0297	0.0124	0.3185	-0.0094	0.2718	26.1708	21.154	190.1203
11	0.8787	-0.1063	-0.1269	1.5344	-0.3645	1.3082	-0.0254	0.098	-0.2815	0.0853	0.0197	0.2884	0.0555	-0.0284	0	0.2907	0.0187	0.051	0.3479	-0.0134	0.3942	16.2438	20.2346	190.0563
12	1.1809	0.4831	-0.3877	1.625	-0.0998	1.2335	0.0339	-0.0889	-0.1081	0.0372	-0.0417	-0.1568	-0.015	0.0674	0	0.3032	-0.0059	-0.0228	0.3019	0.0058	0.2841	57.4834	18.0886	194.996
13	0.8811	-0.6243	-0.0514	0.3591	0.1239	0.0182	0.2051	0.3468	-0.2289	-0.0658	-0.1976	0.0524	0.1399	-0.1013	-0.0007	0.4582	0.0308	0.0329	0.4891	-0.0548	0.3291	39.8249	28.207	162.9546
14	0.5317	-0.1193	-0.2988	0.2698	-0.2845	0.6488	0.0211	0.1739	-0.0746	-0.1395	-0.0861	0.0306	0.0557	0.382	-0	0.4458	0.0086	0.0041	0.4456	-0.0234	0.4196	63.8492	23.224	174.5083
15	0.9145	0.0316	0.3989	0.5187	0.2058	0.8191	0.0655	0.2336	-0.2113	-0.12	-0.0982	-0.0849	0.0545	0.134	-0	0.3955	0.0684	0.0307	0.4277	-0.0986	0.3258	58.6446	17.5171	169.1486
16	0.5609	-0.1032	0.3541	0.2079	0.2621	0.688	0.0616	0.2814	-0.1928	-0.0243	-0.1657	0.0883	0.0132	-0.1955	-0	0.3934	0.0338	0.0307	0.4489	-0.0321	0.3212	55.0646	29.899	167.8745

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 431:477)

-
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 , 6 types, 614 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 , 6 types, 614 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 , 6 types, 614 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