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

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Basic information

Entry
Database: PDB / ID: 5jmq
TitleCrystal Structure of Mus musculus Protein Arginine Methyltransferase 2 with CP3
ComponentsProtein arginine N-methyltransferase 2
KeywordsTRANSFERASE / S-ADENOSYL L-METHIONINE
Function / homology
Function and homology information


protein-arginine N-methyltransferase activity / methylation
Similarity search - Function
Methyltransferase small domain / Methyltransferase small domain / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / SH3 domain / Vaccinia Virus protein VP39 / Distorted Sandwich / Src homology 3 domains ...Methyltransferase small domain / Methyltransferase small domain / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / SH3 domain / Vaccinia Virus protein VP39 / Distorted Sandwich / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-6LC / Protein arginine N-methyltransferase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.795 Å
AuthorsCura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J.
CitationJournal: 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
DepositionApr 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.2Mar 30, 2022Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.3Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4899
Polymers50,6361
Non-polymers8528
Water5,783321
1
A: Protein arginine N-methyltransferase 2
hetero molecules

A: Protein arginine N-methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,97718
Polymers101,2732
Non-polymers1,70516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6160 Å2
ΔGint-38 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.700, 114.685, 132.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-676-

HOH

21A-917-

HOH

31A-921-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein arginine N-methyltransferase 2


Mass: 50636.277 Da / Num. of mol.: 1 / Mutation: R445W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prmt2, Hrmt1l1, mCG_3122 / Plasmid: pDEST20 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3UKX1

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Non-polymers , 6 types, 329 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-6LC / 9-[(5E)-7-carbamimidamido-5,6,7-trideoxy-beta-D-ribo-hept-5-enofuranosyl]-9H-purin-6-amine


Mass: 334.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 22% PEG6000, 100mM CaCl2, 100mM HEPES pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.79→44.05 Å / Num. obs: 46366 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 28.76 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.113 / Net I/σ(I): 9.8
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.957 / Mean I/σ(I) obs: 0.7 / Num. unique all: 12010 / % possible all: 84.9

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Processing

Software
NameVersionClassification
PHENIXdev_1980refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FUB

5fub


Resolution: 1.795→43.309 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.38
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 2320 5.01 %Random selection
Rwork0.1792 ---
obs0.1803 46333 98.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 39.4 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 34 Å2
Refinement stepCycle: LAST / Resolution: 1.795→43.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 55 321 3099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062851
X-RAY DIFFRACTIONf_angle_d0.8783869
X-RAY DIFFRACTIONf_dihedral_angle_d13.8371036
X-RAY DIFFRACTIONf_chiral_restr0.039433
X-RAY DIFFRACTIONf_plane_restr0.004499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7945-1.83120.39161140.36162187X-RAY DIFFRACTION84
1.8312-1.8710.32051260.32742580X-RAY DIFFRACTION99
1.871-1.91450.33041380.29082534X-RAY DIFFRACTION99
1.9145-1.96240.26831370.27152587X-RAY DIFFRACTION99
1.9624-2.01550.26991320.23982580X-RAY DIFFRACTION99
2.0155-2.07480.22461250.2282606X-RAY DIFFRACTION99
2.0748-2.14170.27271550.22862554X-RAY DIFFRACTION99
2.1417-2.21830.24391200.21812605X-RAY DIFFRACTION99
2.2183-2.30710.20521520.17832590X-RAY DIFFRACTION100
2.3071-2.41210.21391500.17352573X-RAY DIFFRACTION100
2.4121-2.53920.21361260.17122654X-RAY DIFFRACTION100
2.5392-2.69830.1911400.17062596X-RAY DIFFRACTION100
2.6983-2.90660.18971230.1682638X-RAY DIFFRACTION100
2.9066-3.1990.17781470.17442621X-RAY DIFFRACTION100
3.199-3.66170.19861460.16092661X-RAY DIFFRACTION100
3.6617-4.61250.14191390.13832668X-RAY DIFFRACTION100
4.6125-43.32180.19621500.1612779X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.5154-0.32240.41962.2302-0.18351.5021-0.0640.02890.1180.1004-0.0134-0.0394-0.13150.12560.07860.1858-0.00440.01640.2069-0.00650.2093-19.332713.1936-22.9554
20.80140.5042-1.81070.8023-2.17017.6629-0.1058-0.109-0.01650.0511-0.0633-0.18380.27970.0480.14310.28580.03980.04660.1729-0.03210.2586-10.32-15.9133-2.0568
30.5994-0.48340.4892.3066-0.68570.47340.02140.1091-0.0784-0.2085-0.0967-0.14140.20270.12040.08860.23580.05750.06430.2515-0.02750.2244-11.2563-10.5643-21.2295
49.5379-9.0299-2.90868.79223.27772.0382-0.2340.1646-0.8560.5173-0.07620.86010.2958-0.04690.34340.28790.03850.05420.2299-0.01440.2721-13.5602-23.7075-14.9635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 107 through 255 )
2X-RAY DIFFRACTION2chain 'A' and (resid 256 through 307 )
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 426 )
4X-RAY DIFFRACTION4chain 'A' and (resid 427 through 445 )

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