PDB-8pjd: Crystal Structure of Mus musculus Protein Arginine Methyltransfer...

ID or keywords:

Entry

Database: PDB / ID: 8pjd

Title

Crystal Structure of Mus musculus Protein Arginine Methyltransferase 2 94-445

Components

Protein arginine N-methyltransferase 2

Keywords

TRANSFERASE / protein arginine N-methyltransferase / PRMT / SH3 / methylation / transcription

Function / homology

Function and homology information

protein-arginine N-methyltransferase activity / methylation / metal ion binding
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Cura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal Structure of Mus musculus Protein Arginine Methyltransferase 2 94-445
Authors: Cura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J.

History

Deposition	Jun 23, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8pjd.cif.gz	225.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8pjd.ent.gz	179.8 KB	Display	PDB format
PDBx/mmJSON format	8pjd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pjd_validation.pdf.gz	799.5 KB	Display	wwPDB validaton report
Full document	8pjd_full_validation.pdf.gz	801.8 KB	Display
Data in XML	8pjd_validation.xml.gz	19.5 KB	Display
Data in CIF	8pjd_validation.cif.gz	29.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pj/8pjd ftp://data.pdbj.org/pub/pdb/validation_reports/pj/8pjd	HTTPS FTP

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Related structure data

Similar structure data	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

Deposited unit

A: Protein arginine N-methyltransferase 2

hetero molecules

41.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein arginine N-methyltransferase 2

hetero molecules

A: Protein arginine N-methyltransferase 2

hetero molecules

defined by author
Evidence: mass spectrometry
82.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	65.052, 115.980, 133.718
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-748- HOH
2	1	A-1003- HOH
3	1	A-1005- HOH

#1: Protein	Protein arginine N-methyltransferase 2 Mass: 40623.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prmt2, Hrmt1l1 Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: Q3UKX1
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.11 Å³/Da / Density % sol: 60.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 / Details: 1.3M AcONa pH5.3

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
Detector	Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 4, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 1.6→29.25 Å / Num. obs: 65279 / % possible obs: 97.5 % / Redundancy: 7 % / B_iso Wilson estimate: 22.5 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.075 / R_pim(I) all: 0.021 / R_rim(I) all: 0.07845 / Net I/σ(I): 17.7
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 9.2 % / R_merge(I) obs: 2.384 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2584 / CC_1/2: 0.38 / CC star: 0.59 / R_pim(I) all: 0.808 / R_rim(I) all: 2.527 / % possible all: 77.85

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_4958: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→29.25 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1891	3303	5.06 %
R_work	0.1714	-	-
obs	0.1723	65234	97.5 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.6→29.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2781	0	44	405	3230

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2896
X-RAY DIFFRACTION	f_angle_d	1.005	3941
X-RAY DIFFRACTION	f_dihedral_angle_d	15.291	1034
X-RAY DIFFRACTION	f_chiral_restr	0.055	441
X-RAY DIFFRACTION	f_plane_restr	0.009	500

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 (%)
1.6-1.62	0.3822	115	0.3332	2064	X-RAY DIFFRACTION	78
1.62-1.65	0.3698	116	0.3068	2119	X-RAY DIFFRACTION	83
1.65-1.67	0.3103	130	0.2758	2300	X-RAY DIFFRACTION	87
1.67-1.7	0.2834	136	0.2614	2470	X-RAY DIFFRACTION	94
1.7-1.73	0.2308	135	0.2363	2599	X-RAY DIFFRACTION	100
1.73-1.76	0.2373	119	0.2145	2655	X-RAY DIFFRACTION	100
1.76-1.79	0.2583	162	0.2174	2581	X-RAY DIFFRACTION	100
1.79-1.83	0.2253	149	0.2054	2621	X-RAY DIFFRACTION	100
1.83-1.87	0.2623	145	0.2105	2605	X-RAY DIFFRACTION	100
1.87-1.91	0.2142	137	0.2029	2656	X-RAY DIFFRACTION	100
1.91-1.96	0.2275	131	0.19	2642	X-RAY DIFFRACTION	100
1.96-2.02	0.1887	135	0.1671	2615	X-RAY DIFFRACTION	100
2.02-2.08	0.1857	133	0.1694	2648	X-RAY DIFFRACTION	100
2.08-2.14	0.1726	155	0.1621	2626	X-RAY DIFFRACTION	100
2.14-2.22	0.1787	135	0.1592	2647	X-RAY DIFFRACTION	100
2.22-2.31	0.1618	142	0.158	2622	X-RAY DIFFRACTION	100
2.31-2.41	0.1829	153	0.1618	2629	X-RAY DIFFRACTION	100
2.41-2.54	0.1755	125	0.1574	2650	X-RAY DIFFRACTION	100
2.54-2.7	0.1933	134	0.1649	2674	X-RAY DIFFRACTION	100
2.7-2.91	0.1658	125	0.1631	2676	X-RAY DIFFRACTION	100
2.91-3.2	0.1671	155	0.1701	2611	X-RAY DIFFRACTION	99
3.2-3.66	0.1913	145	0.166	2697	X-RAY DIFFRACTION	100
3.66-4.61	0.1548	138	0.143	2708	X-RAY DIFFRACTION	100
4.61-29.25	0.2019	153	0.1777	2816	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	3.3633	2.2535	2.4184	7.7908	1.535	7.3728	0.0347	-0.5218	-0.0999	0.6755	-0.3121	0.9851	0.111	-0.6127	0.1696	0.2126	0.0502	0.0817	0.2561	-0.0233	0.3556	-31.7613	3.993	-12.4027
2	1.6043	-0.2744	0.6162	1.446	-0.3859	1.8737	-0.0442	0.1555	0.1597	0.0777	-0.0693	-0.1287	-0.1296	0.2771	0.1066	0.1576	-0.0013	-0.0009	0.1891	0.0082	0.1787	-17.9999	14.5198	-24.1795
3	0.7246	0.1697	-0.9609	0.6979	-1.0972	3.1204	-0.0051	-0.0735	-0.084	0.0548	-0.1248	0.0087	0.1206	0.1289	0.138	0.2708	0.0339	0.0449	0.1937	-0.0204	0.2452	-10.2051	-15.9264	-2.4069
4	0.9292	-1.1592	0.9224	1.4274	-1.0792	0.6682	0.2022	0.3078	-0.048	-0.3426	-0.2895	-0.0672	0.3034	0.2304	0.0979	0.3449	0.1088	0.0271	0.3235	-0.0365	0.2776	-10.8866	-12.752	-24.2087
5	1.4388	-0.9152	0.3889	2.4321	-0.2235	0.1189	0.0563	0.1315	-0.1256	-0.1374	-0.1109	0.0809	0.124	0.0833	0.0577	0.2427	0.0695	0.0245	0.2528	-0.0308	0.1664	-12.0066	-11.9736	-19.1857
6	0.4521	3.3046	-1.0788	2.0005	-7.9201	2.5929	0.412	-0.083	1.4895	0.6367	0.0831	0.6066	-0.6267	-0.1413	-0.4578	0.504	0.0332	0.0726	0.4082	-0.0769	0.5918	-24.2022	-1.8497	-8.1177

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 104 through 118 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 120 through 255 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 256 through 307 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 308 through 349 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 350 through 445 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 90 through 94 )

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