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

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Basic information

Entry
Database: PDB / ID: 8bva
TitleCrystal Structure of Mus musculus Protein Arginine Methyltransferase 2 in complex with RSF1_114-126
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


protein-arginine N-methyltransferase activity / methylation / RNA binding
Similarity search - Function
Methyltransferase small domain / Methyltransferase small domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / SH3 domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...Methyltransferase small domain / Methyltransferase small domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / SH3 domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Nucleotide-binding alpha-beta plait domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / Chem-QVR / L(+)-TARTARIC ACID / RNA-binding protein Rsf1 / Protein arginine N-methyltransferase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Spodoptera aff. frugiperda 2 BOLD-2017 (butterflies/moths)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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_114-126
Authors: Cura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J.
History
DepositionDec 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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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
B: RNA-binding protein Rsf1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0055
Polymers40,5382
Non-polymers4663
Water1,53185
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)82,00910
Polymers81,0764
Non-polymers9336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7070 Å2
ΔGint-45 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.711, 114.409, 133.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Protein arginine N-methyltransferase 2


Mass: 39067.609 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 / SFRICE_009903


Mass: 1470.510 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Spodoptera aff. frugiperda 2 BOLD-2017 (butterflies/moths)
References: UniProt: A0A2H1V327

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Non-polymers , 4 types, 88 molecules

#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K
#5: 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


Mass: 277.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N5O3
Source: (synth.) Spodoptera aff. frugiperda 2 BOLD-2017 (butterflies/moths)
Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.2M ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.19→29.55 Å / Num. obs: 25946 / % possible obs: 99.1 % / Redundancy: 13.8 % / Biso Wilson estimate: 44.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.11 / Χ2: 1 / Net I/σ(I): 14.9
Reflection shellResolution: 2.19→2.26 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.48 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2056 / CC1/2: 0.686 / Rrim(I) all: 1.541 / Χ2: 0.97 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.20.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FUL

5ful


Resolution: 2.19→29.55 Å / SU ML: 0.2088 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.124
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2016 1295 5 %
Rwork0.1769 24611 -
obs0.1783 25906 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.24 Å2
Refinement stepCycle: LAST / Resolution: 2.19→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 11 85 2874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562863
X-RAY DIFFRACTIONf_angle_d0.72693898
X-RAY DIFFRACTIONf_chiral_restr0.0454438
X-RAY DIFFRACTIONf_plane_restr0.0064507
X-RAY DIFFRACTIONf_dihedral_angle_d15.95771045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.280.28721360.26932544X-RAY DIFFRACTION93.67
2.28-2.380.27741500.23552695X-RAY DIFFRACTION99.82
2.38-2.510.26761380.22552720X-RAY DIFFRACTION99.97
2.51-2.670.2411370.20482747X-RAY DIFFRACTION100
2.67-2.870.2161320.20312775X-RAY DIFFRACTION99.97
2.87-3.160.22291620.20592726X-RAY DIFFRACTION99.97
3.16-3.620.20951420.18032756X-RAY DIFFRACTION99.9
3.62-4.550.16971410.1462746X-RAY DIFFRACTION98.33
4.55-29.550.17881570.15642902X-RAY DIFFRACTION99.93
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)
11.74323503168-0.4220803672050.9381592616573.580318993610.01359351991592.69952232886-0.112268179790.02861207104840.07354861126130.15714904236-0.0275401184122-0.152289894786-0.1972646767370.06916143526170.1383822787760.3217913402470.009713370751460.03820813286780.3123640882-0.004471605812880.339061708886-19.490518877412.7332105613-23.1191452468
20.7771973286820.132014979489-1.191941117610.0952103017967-0.7751523477053.65204143054-0.105426169115-0.0254355055726-0.0464470898005-0.0113769597936-0.0863827344269-0.2162175477020.289577948940.09630626221650.2177654514670.5081883440850.04174014597290.09231858799720.349261322343-0.007060215345990.541648382979-10.1479720999-15.9885793264-1.86107075467
30.438614085138-0.3085324057050.7116016544032.58857542856-0.8336088207120.591492304674-0.01757226771310.139880547947-0.098490082297-0.220229940084-0.110371520164-0.2661097063710.2135673946760.1346270652010.1322080370010.4006529339220.05463297528460.137272872640.411861043756-0.0385552040040.413197947239-11.176198218-10.8189904995-21.1294273393
41.84356873607-1.325980869680.9803622681074.5475370296-0.4340674954781.388739980840.03803457464880.221136485239-0.2893201674760.135970111954-0.04466243259840.08714111843530.16019988758-0.0665718280688-0.1295044676770.406637374124-0.0005311899220530.1115419282210.356056836262-0.02727552350160.385659667034-13.2403155833-24.1666421278-15.0420436666
52.01000102896-5.14351585989-2.471139944325.89340930756-1.50735547595.21395196357-0.055609674893-0.451997954654-1.397766581021.46828453432-0.08327489389510.07085134323290.2806653417310.4135320420710.1290824772180.648502755432-0.0777092433735-0.04813928908340.4024532811250.05952063300350.675136810089-20.26361297354.60423925968-14.27265888
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 106 through 255)AA106 - 2551 - 150
22(chain 'A' and resid 256 through 307)AA256 - 307151 - 202
33(chain 'A' and resid 308 through 426)AA308 - 426203 - 321
44(chain 'A' and resid 427 through 445)AA427 - 445322 - 340
55(chain 'B' and resid 117 through 121)BC117 - 1211 - 5

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