PDB-4c03: Crystal structure of M. musculus protein arginine methyltransfera...

ID or keywords:

Entry

Database: PDB / ID: 4c03

Title

Crystal structure of M. musculus protein arginine methyltransferase PRMT6 reduced

Components

PROTEIN ARGININE N-METHYLTRANSFERASE 6

Keywords

TRANSFERASE / S-ADENOSYL-L-METHIONINE

Function / homology

Function and homology information

histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity ...
Similarity search - Function

Biological species

MUS MUSCULUS (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.58 Å

Authors

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

Citation

Journal: J.Struct.Biol. / Year: 2015
Title: Functional Insights from High Resolution Structures of Mouse Protein Arginine Methyltransferase 6.
Authors: Bonnefond, L. / Stojko, J. / Mailliot, J. / Troffer-Charlier, N. / Cura, V. / Wurtz, J.M. / Cianferani, S. / Cavarelli, J.

History

Deposition	Jul 31, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 30, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 1, 2015	Group: Database references
Revision 1.2	Aug 12, 2015	Group: Database references
Revision 2.0	Dec 20, 2023	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4c03.cif.gz	409.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4c03.ent.gz	338.9 KB	Display	PDB format
PDBx/mmJSON format	4c03.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4c03_validation.pdf.gz	979.3 KB	Display	wwPDB validaton report
Full document	4c03_full_validation.pdf.gz	968.7 KB	Display
Data in XML	4c03_validation.xml.gz	31 KB	Display
Data in CIF	4c03_validation.cif.gz	46.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c0/4c03 ftp://data.pdbj.org/pub/pdb/validation_reports/c0/4c03	HTTPS FTP

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Related structure data

Related structure data	4c04C 4c05C 4c06C 4c07C 4c08C 2y1wS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6sq4-d 6sqk-d 6sq3-d 6sqh-d 5hzm-1 4hc4-1 5lv4-1 7nr4-2 4qpp-2 6sqi-1 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	#87 - Mar 2007 Zinc Fingers similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1)

Deposited unit

A: PROTEIN ARGININE N-METHYLTRANSFERASE 6

B: PROTEIN ARGININE N-METHYLTRANSFERASE 6

hetero molecules

85.4 kDa, 2 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)	118.722, 143.340, 41.958
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	PROTEIN ARGININE N-METHYLTRANSFERASE 6 / HISTONE-ARGININE N-METHYLTRANSFERASE PRMT6 Mass: 42321.793 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) References: UniProt: Q6NZB1, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Chemical	ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₇O₅
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 591 / 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: 2.41 Å³/Da / Density % sol: 48.96 % / Description: NONE
Crystal grow	pH: 7 / Details: 100 MM HEPES PH 7.0, 200 MM MGCL2, 25% PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9537
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.58→39.56 Å / Num. obs: 98190 / % possible obs: 99 % / Observed criterion σ(I): 0.8 / Redundancy: 6.3 % / R_merge(I) obs: 0.11 / Net I/σ(I): 8.71
Reflection shell	Resolution: 1.58→1.64 Å / Redundancy: 4.4 % / R_merge(I) obs: 1.01 / Mean I/σ(I) obs: 0.99 / % possible all: 90.7

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y1W

2y1w

Resolution: 1.58→39.56 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 21.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1914	4909	5 %
R_work	0.1601	-	-
obs	0.1617	98176	99.03 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.58→39.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5234	0	54	591	5879

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	5526
X-RAY DIFFRACTION	f_angle_d	1.281	7539
X-RAY DIFFRACTION	f_dihedral_angle_d	14.252	2042
X-RAY DIFFRACTION	f_chiral_restr	0.054	836
X-RAY DIFFRACTION	f_plane_restr	0.006	973

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 (%)
1.5802-1.5981	0.3055	125	0.2925	2428	X-RAY DIFFRACTION	79
1.5981-1.6169	0.3176	161	0.2666	3019	X-RAY DIFFRACTION	95
1.6169-1.6366	0.2758	157	0.2642	2984	X-RAY DIFFRACTION	98
1.6366-1.6574	0.2976	164	0.2448	3110	X-RAY DIFFRACTION	100
1.6574-1.6792	0.3087	164	0.2325	3109	X-RAY DIFFRACTION	100
1.6792-1.7022	0.2417	162	0.2253	3071	X-RAY DIFFRACTION	100
1.7022-1.7265	0.2486	162	0.2127	3077	X-RAY DIFFRACTION	100
1.7265-1.7523	0.2332	166	0.1996	3156	X-RAY DIFFRACTION	100
1.7523-1.7796	0.233	161	0.191	3055	X-RAY DIFFRACTION	100
1.7796-1.8088	0.2135	163	0.1932	3101	X-RAY DIFFRACTION	100
1.8088-1.84	0.2096	165	0.183	3137	X-RAY DIFFRACTION	100
1.84-1.8735	0.2404	162	0.1837	3068	X-RAY DIFFRACTION	100
1.8735-1.9095	0.2313	167	0.1802	3172	X-RAY DIFFRACTION	100
1.9095-1.9485	0.2468	161	0.1741	3061	X-RAY DIFFRACTION	100
1.9485-1.9908	0.2072	165	0.1727	3147	X-RAY DIFFRACTION	100
1.9908-2.0372	0.1903	163	0.1556	3089	X-RAY DIFFRACTION	100
2.0372-2.0881	0.1727	165	0.154	3128	X-RAY DIFFRACTION	100
2.0881-2.1446	0.1999	165	0.1597	3135	X-RAY DIFFRACTION	100
2.1446-2.2077	0.1948	166	0.1551	3156	X-RAY DIFFRACTION	100
2.2077-2.2789	0.2005	162	0.1473	3075	X-RAY DIFFRACTION	100
2.2789-2.3603	0.1846	166	0.147	3156	X-RAY DIFFRACTION	100
2.3603-2.4548	0.1976	166	0.1499	3155	X-RAY DIFFRACTION	100
2.4548-2.5665	0.1684	164	0.1489	3127	X-RAY DIFFRACTION	100
2.5665-2.7018	0.1784	166	0.1478	3152	X-RAY DIFFRACTION	100
2.7018-2.8711	0.1829	167	0.1557	3167	X-RAY DIFFRACTION	100
2.8711-3.0927	0.1767	167	0.1611	3171	X-RAY DIFFRACTION	100
3.0927-3.4037	0.1919	168	0.1562	3203	X-RAY DIFFRACTION	100
3.4037-3.8959	0.1804	169	0.1403	3200	X-RAY DIFFRACTION	100
3.8959-4.9069	0.1324	171	0.1295	3248	X-RAY DIFFRACTION	100
4.9069-39.5725	0.1948	179	0.1647	3410	X-RAY DIFFRACTION	100

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	8.2743	1.69	2.3763	6.1923	2.8962	7.9278	-0.3054	1.4428	0.0266	-1.3763	-0.3333	0.4406	-0.7584	-0.3323	0.6219	0.5566	0.0299	-0.0402	0.6358	-0.0121	0.4105	27.9264	20.5473	-0.811
2	2.0316	-0.0693	-0.1265	2.5128	0.7296	1.1548	-0.0509	-0.0923	-0.0614	0.1257	0.0716	-0.1635	-0.0236	0.0444	-0.0101	0.1213	-0.0058	-0.0152	0.1522	0.0023	0.1062	36.7895	13.7572	18.2818
3	5.104	-1.6507	-0.2307	1.1769	-0.0827	0.5272	-0.0519	0.0638	-0.2275	0.0156	0.011	0.083	0.011	0.001	0.0416	0.1574	-0.025	0.0082	0.1462	-0.0211	0.1579	25.869	5.7823	12.2642
4	4.7015	-5.6685	-0.766	6.835	0.9566	0.1297	-0.0019	-0.1438	-0.1947	-0.0482	0.1375	0.1479	-0.0479	0.021	-0.0958	0.2405	0.0009	0.0452	0.1867	0.0526	0.284	-4.0333	32.5446	11.6791
5	5.5303	0.0259	-2.8363	6.4878	1.1494	6.8676	-0.0139	-0.2129	-0.0679	0.6598	-0.0389	0.4064	0.0291	-0.1288	-0.0228	0.0603	0.007	-0.0359	0.1935	0.01	0.1846	5.5594	11.8562	19.2097
6	3.4927	-0.2016	0.7399	1.5066	-0.0572	1.2821	0.0024	-0.0854	-0.2376	0.0657	0.0395	0.2989	0.0356	-0.049	-0.0191	0.1439	-0.0074	0.0501	0.1335	0.0164	0.2163	8.9226	8.6913	16.1675
7	5.9175	0.3084	-0.7674	2.8465	-0.2579	3.6111	-0.0645	0.497	-0.1587	-0.3908	0.0468	0.2856	-0.1016	0.0537	0.0001	0.1857	0.0216	-0.0375	0.1808	-0.0004	0.239	5.3997	11.7768	2.9123
8	7.1889	0.2385	-5.1226	2.5953	-1.4687	4.2967	0.1133	0.938	-0.5839	-0.4995	-0.0332	-0.8216	1.2599	1.195	-0.0902	0.6068	0.1012	-0.086	0.7544	-0.0875	0.8089	6.8436	40.4177	-4.1943
9	2.1288	-0.2879	-0.1517	2.0838	-0.4323	2.5766	0.01	0.0235	-0.1804	-0.0755	-0.0104	-0.0291	0.2115	-0.0526	-0.004	0.1279	-0.0066	-0.0008	0.1368	0.0134	0.144	-6.2947	49.2914	4.6893
10	6.7486	-2.141	4.1793	0.6973	-0.7544	2.5836	-0.0632	0.2813	0.1639	-0.0328	-0.0765	-0.1219	-0.0524	0.1683	0.1309	0.1601	-0.0429	-0.0136	0.2107	0.0743	0.21	5.7732	56.9825	1.6571
11	2.3032	-2.2872	1.8882	3.7488	-3.2843	3.2247	-0.1003	-0.1481	0.1425	0.0443	0.1101	-0.0614	-0.0957	-0.1303	-0.0498	0.2138	0.0037	-0.0363	0.1873	-0.0429	0.1666	32.3409	32.2058	20.206
12	4.5505	-0.5337	1.743	3.116	0.1056	4.0622	-0.2228	-0.1608	0.5409	0.4356	0.3519	-0.0174	-0.3173	-0.2181	-0.1329	0.1292	0.0057	0.0189	0.2117	0.0289	0.2264	18.4598	56.5606	13.6347
13	4.0371	-0.2242	0.5103	2.765	0.1187	1.3427	-0.0701	-0.0916	0.2055	0.0823	0.1469	-0.1616	-0.1149	0.018	-0.0587	0.175	0.0022	-0.0554	0.146	0.0002	0.173	21.9641	54.1103	13.6759
14	7.006	1.6314	4.6489	5.4622	1.9474	8.7384	-0.1318	0.3498	-0.0302	-0.4429	0.2314	-0.4555	-0.0535	0.3561	-0.1174	0.1614	0.0329	0.0225	0.1595	-0.0089	0.2242	29.8676	50.1036	5.5674

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 41:54)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 55:147)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 148:201)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 202:240)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 241:258)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 259:342)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 343:377)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 47:54)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 55:146)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 147:200)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 201:240)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 241:266)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 267:350)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 351:377)

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