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- PDB-8c1j: Crystal Structure of Mus musculus Protein Arginine Methyltransfer... -

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Basic information

Entry
Database: PDB / ID: 8c1j
TitleCrystal Structure of Mus musculus Protein Arginine Methyltransferase 2 in complex with RSF1_18-30
Components
  • Protein arginine N-methyltransferase 2
  • RNA-binding protein Rsf1-like
KeywordsTRANSFERASE / protein arginine N-methyltransferase / PRMT / SH3 / methylation / TRANSCRIPTION
Function / homology
Function and homology information


type I protein arginine methyltransferase / protein-arginine N-methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Methyltransferase small domain / Methyltransferase small domain / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...Methyltransferase small domain / Methyltransferase small domain / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-QVR / Protein arginine N-methyltransferase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of Mus musculus Protein Arginine Methyltransferase 2 in complex with RSF1_18-30
Authors: Cura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J.
History
DepositionDec 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 2
B: RNA-binding protein Rsf1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5613
Polymers42,2842
Non-polymers2771
Water2,432135
1
A: Protein arginine N-methyltransferase 2
B: RNA-binding protein Rsf1-like
hetero molecules

A: Protein arginine N-methyltransferase 2
B: RNA-binding protein Rsf1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1236
Polymers84,5684
Non-polymers5552
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)66.178, 114.964, 133.181
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-525-

HOH

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Components

#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: Protein/peptide RNA-binding protein Rsf1-like


Mass: 1660.823 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
#3: Chemical ChemComp-QVR / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol / SFRICE_009903


Mass: 277.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N5O3
Source: (synth.) Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.1M ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→29.69 Å / Num. obs: 34584 / % possible obs: 99.6 % / Redundancy: 26.7 % / Biso Wilson estimate: 48.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.019 / Rrim(I) all: 0.101 / Net I/σ(I): 19.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 23.1 % / Rmerge(I) obs: 3.41 / Mean I/σ(I) obs: 1 / Num. unique obs: 2361 / CC1/2: 0.399 / Rpim(I) all: 0.708 / Rrim(I) all: 3.488 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.69 Å / SU ML: 0.2375 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1141
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2064 1730 5.01 %
Rwork0.1796 32800 -
obs0.181 34530 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54 Å2
Refinement stepCycle: LAST / Resolution: 2→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 0 135 2941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01252882
X-RAY DIFFRACTIONf_angle_d0.99623923
X-RAY DIFFRACTIONf_chiral_restr0.064440
X-RAY DIFFRACTIONf_plane_restr0.0083510
X-RAY DIFFRACTIONf_dihedral_angle_d15.17271057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.33611350.32242569X-RAY DIFFRACTION95.08
2.06-2.130.29261400.27192716X-RAY DIFFRACTION99.9
2.13-2.20.26611470.23992693X-RAY DIFFRACTION99.79
2.2-2.290.30281480.22262732X-RAY DIFFRACTION99.83
2.29-2.390.24271490.2192694X-RAY DIFFRACTION99.96
2.39-2.520.25251400.20372715X-RAY DIFFRACTION99.96
2.52-2.680.23281340.19782741X-RAY DIFFRACTION99.9
2.68-2.880.21571330.19282776X-RAY DIFFRACTION99.9
2.88-3.170.22021610.2082709X-RAY DIFFRACTION99.97
3.17-3.630.23081410.18522757X-RAY DIFFRACTION100
3.63-4.570.17751450.152795X-RAY DIFFRACTION100
4.57-29.690.1681570.15282903X-RAY DIFFRACTION99.97
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)
12.03604798575-0.4423831808151.03570248653.16271882175-0.1905381205712.44663379728-0.140006248683-0.02413395345020.07572332515880.188163650871-0.0252172767797-0.0467966868356-0.2169172405890.03710317441860.1611356113790.3846186177950.004350976074910.02148957079260.372088687131-0.009715958973090.396705426404-19.681400965512.9439949206-23.0750813443
20.3353411408320.164539186738-0.6854915297540.914214011852-2.026370198424.78192789602-0.127120705953-0.08413328055530.03433394166010.0668310133594-0.0535899574644-0.1423305113550.131245939881-0.06933404297520.1791225725810.5310448020640.06326318485890.1155744335040.400478952217-0.007063104553580.534819999676-10.3221770971-16.0659265639-1.86345908299
30.264055269198-0.4752123042661.002974848362.84752062128-0.9416822526080.6027253541810.001806722274170.0910681610188-0.123713380895-0.172415168689-0.0958669791109-0.1835024263330.2082170576410.08653882008670.08210062988530.4329006439840.05351805850230.1340675112070.4240942777-0.01955332367520.421159399775-11.6177306095-12.5581656321-20.3006631211
43.623326033512.36902619844-5.297342722712.00747637837-6.498093986612.02157658124-0.106251947382-0.454324770665-0.7829136316660.9839361152640.126897105213-0.3999689004460.1384218164320.802608147194-0.05121419626550.8263941542030.0409647322071-0.1170216224740.644963705875-0.04253719417550.687653596732-22.55409569522.13633693536-12.116297863
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDEnd label seq-ID
11chain 'A' and (resid 106 through 255 )AA106 - 2551 - 150
22chain 'A' and (resid 256 through 307 )AA256 - 307151 - 202
33chain 'A' and (resid 308 through 445 )AA308 - 445203 - 340
44chain 'B' and (resid 24 through 28 )BB24 - 286

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