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- PDB-4ryl: Human Protein Arginine Methyltransferase 3 in complex with 1-isoq... -

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Basic information

Entry
Database: PDB / ID: 4ryl
TitleHuman Protein Arginine Methyltransferase 3 in complex with 1-isoquinolin-6-yl-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea
ComponentsPRMT3 protein
KeywordsTRANSFERASE / PRMT3 / SGC707 / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


protein-arginine omega-N monomethyltransferase activity / negative regulation of retinoic acid biosynthetic process / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein-arginine N-methyltransferase activity / Protein methylation / negative regulation of protein ubiquitination / methyltransferase activity / RMTs methylate histone arginines / ribosome binding ...protein-arginine omega-N monomethyltransferase activity / negative regulation of retinoic acid biosynthetic process / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein-arginine N-methyltransferase activity / Protein methylation / negative regulation of protein ubiquitination / methyltransferase activity / RMTs methylate histone arginines / ribosome binding / methylation / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Protein arginine N-methyltransferase 3, C2H2 zinc finger domain / Protein arginine N-methyltransferase 3, C2H2 zinc finger / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Zinc finger C2H2 superfamily ...: / : / Protein arginine N-methyltransferase 3, C2H2 zinc finger domain / Protein arginine N-methyltransferase 3, C2H2 zinc finger / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-3ZG / Protein arginine N-methyltransferase 3 / PRMT3 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDong, A. / Dobrovetsky, E. / Kaniskan, H.U. / Szewczyk, M. / Yu, Z. / Eram, M.S. / Yang, X. / Schmidt, K. / Luo, X. / Dai, M. ...Dong, A. / Dobrovetsky, E. / Kaniskan, H.U. / Szewczyk, M. / Yu, Z. / Eram, M.S. / Yang, X. / Schmidt, K. / Luo, X. / Dai, M. / He, F. / Zang, I. / Lin, Y. / Kennedy, S. / Li, F. / Tempel, W. / Smil, D. / Min, S.J. / Landon, M. / Lin-Jones, J. / Huang, X.P. / Roth, B.L. / Schapira, M. / Atadja, P. / Barsyte-Lovejoy, D. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Brown, P.J. / Zhao, K. / Jin, J. / Vedadi, M. / Structural Genomics Consortium (SGC)
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: A Potent, Selective and Cell-Active Allosteric Inhibitor of Protein Arginine Methyltransferase 3 (PRMT3).
Authors: Kaniskan, H.U. / Szewczyk, M.M. / Yu, Z. / Eram, M.S. / Yang, X. / Schmidt, K. / Luo, X. / Dai, M. / He, F. / Zang, I. / Lin, Y. / Kennedy, S. / Li, F. / Dobrovetsky, E. / Dong, A. / Smil, D. ...Authors: Kaniskan, H.U. / Szewczyk, M.M. / Yu, Z. / Eram, M.S. / Yang, X. / Schmidt, K. / Luo, X. / Dai, M. / He, F. / Zang, I. / Lin, Y. / Kennedy, S. / Li, F. / Dobrovetsky, E. / Dong, A. / Smil, D. / Min, S.J. / Landon, M. / Lin-Jones, J. / Huang, X.P. / Roth, B.L. / Schapira, M. / Atadja, P. / Barsyte-Lovejoy, D. / Arrowsmith, C.H. / Brown, P.J. / Zhao, K. / Jin, J. / Vedadi, M.
History
DepositionDec 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references / Structure summary
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRMT3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5804
Polymers38,2821
Non-polymers2983
Water3,045169
1
A: PRMT3 protein
hetero molecules

A: PRMT3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1618
Polymers76,5642
Non-polymers5976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3450 Å2
ΔGint-31 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.691, 70.691, 173.559
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PRMT3 protein /


Mass: 38281.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT3 / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-PRAR2 / References: UniProt: Q8WUV3, UniProt: O60678*PLUS
#2: Chemical ChemComp-3ZG / 1-isoquinolin-6-yl-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea


Mass: 298.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N4O2
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350 and 0.2 M di Na tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 26698 / % possible obs: 99.9 % / Redundancy: 14.9 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.099 / Χ2: 0.946 / Net I/σ(I): 30.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.14150.95113070.763199.9
2.14-2.1814.90.79113070.743199.8
2.18-2.22150.74312970.779199.9
2.22-2.26150.55412911.162199.8
2.26-2.31150.70713030.8221100
2.31-2.37150.4713210.8131100
2.37-2.4215.10.43713010.8131100
2.42-2.49150.40813140.8181100
2.49-2.56150.32413080.821100
2.56-2.6515.10.27313300.8311100
2.65-2.7415.10.2313090.8781100
2.74-2.8515.10.18613380.8761100
2.85-2.9815.10.14313290.8991100
2.98-3.1415.10.11113220.9381100
3.14-3.3315.10.08113381.0041100
3.33-3.59150.06713501.1221100
3.59-3.95150.06113571.3961100
3.95-4.52150.04913681.3081100
4.52-5.714.70.04113971.0931100
5.7-5013.30.03315110.995198.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
JDirectordata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Coot0.7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FYT

2fyt


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1988 / WRfactor Rwork: 0.16 / FOM work R set: 0.8305 / SU B: 4.026 / SU ML: 0.107 / SU R Cruickshank DPI: 0.1614 / SU Rfree: 0.1556 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 818 3.1 %RANDOM
Rwork0.1861 ---
all0.1875 ---
obs-25762 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.2 Å2 / Biso mean: 33.717 Å2 / Biso min: 22.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å2-0 Å2-0 Å2
2--0.69 Å2-0 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 24 169 2521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192466
X-RAY DIFFRACTIONr_bond_other_d0.0010.022360
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9523350
X-RAY DIFFRACTIONr_angle_other_deg0.73835444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35824.3397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78615434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.681158
X-RAY DIFFRACTIONr_chiral_restr0.080.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022817
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
X-RAY DIFFRACTIONr_mcbond_it1.9773.2571222
X-RAY DIFFRACTIONr_mcbond_other1.9763.2541220
X-RAY DIFFRACTIONr_mcangle_it2.8364.8651529
LS refinement shellResolution: 2.098→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 51 -
Rwork0.212 1875 -
all-1926 -
obs--99.9 %

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