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- PDB-4qqn: Protein arginine methyltransferase 3 in complex with compound MTV... -

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Basic information

Entry
Database: PDB / ID: 4qqn
TitleProtein arginine methyltransferase 3 in complex with compound MTV044246
ComponentsPRMT3 protein
KeywordsTRANSFERASE / PRMT3 / Structural Genomics / Structural Genomics Consortium / SGC / Epigenetics
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-3BQ / Protein arginine N-methyltransferase 3 / PRMT3 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsDong, A. / Dobrovetsky, E. / Tempel, W. / He, H. / Zhao, K. / Smil, D. / Landon, M. / Luo, X. / Chen, Z. / Dai, M. ...Dong, A. / Dobrovetsky, E. / Tempel, W. / He, H. / Zhao, K. / Smil, D. / Landon, M. / Luo, X. / Chen, Z. / Dai, M. / Yu, Z. / Lin, Y. / Zhang, H. / Zhao, K. / Schapira, M. / Brown, P.J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Structural Genomics Consortium (SGC)
CitationJournal: J. Med. Chem. / Year: 2018
Title: Discovery of Potent and Selective Allosteric Inhibitors of Protein Arginine Methyltransferase 3 (PRMT3).
Authors: Kaniskan, H.U. / Eram, M.S. / Zhao, K. / Szewczyk, M.M. / Yang, X. / Schmidt, K. / Luo, X. / Xiao, S. / Dai, M. / He, F. / Zang, I. / Lin, Y. / Li, F. / Dobrovetsky, E. / Smil, D. / Min, S.J. ...Authors: Kaniskan, H.U. / Eram, M.S. / Zhao, K. / Szewczyk, M.M. / Yang, X. / Schmidt, K. / Luo, X. / Xiao, S. / Dai, M. / He, F. / Zang, I. / Lin, Y. / Li, F. / Dobrovetsky, E. / Smil, D. / Min, S.J. / Lin-Jones, J. / Schapira, M. / Atadja, P. / Li, E. / Barsyte-Lovejoy, D. / Arrowsmith, C.H. / Brown, P.J. / Liu, F. / Yu, Z. / Vedadi, M. / Jin, J.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Sep 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)38,73616
Polymers38,2821
Non-polymers45415
Water2,810156
1
A: PRMT3 protein
hetero molecules

A: PRMT3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,47232
Polymers76,5642
Non-polymers90830
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4070 Å2
ΔGint-57 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.319, 70.319, 172.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#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)-codon plus RIL(Stratagen)
References: UniProt: Q8WUV3, UniProt: O60678*PLUS

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-3BQ / 1-{2-[1-(aminomethyl)cyclohexyl]ethyl}-3-isoquinolin-6-ylurea


Mass: 326.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26N4O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.2 M MgCl2, 0.1 M Tris HCL pH8.5, vapor diffusion hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 27071 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.035 / Net I/σ(I): 25.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.08-2.124.40.70413030.826199.9
2.12-2.155.20.7113240.8171100
2.15-2.25.60.53513290.8291100
2.2-2.246.20.47113050.8221100
2.24-2.296.40.44413380.8591100
2.29-2.346.40.37413300.8561100
2.34-2.46.40.32113110.8611100
2.4-2.476.40.30313390.841100
2.47-2.546.40.25113450.8631100
2.54-2.626.40.20613390.8951100
2.62-2.716.40.17213380.9371100
2.71-2.826.30.13613360.9391100
2.82-2.956.30.11513400.9551100
2.95-3.116.30.07913490.9651100
3.11-3.36.30.06113511.0271100
3.3-3.566.20.04913741.1311100
3.56-3.916.10.04513821.3951100
3.91-4.4860.04613792.0811100
4.48-5.645.80.03814181.7071100
5.64-505.50.02515410.984199.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREP11.1.03phasing
Coot0.7.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HSG

4hsg


Resolution: 2.08→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.614 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 858 3.2 %RANDOM
Rwork0.183 ---
obs0.1839 26987 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.44 Å2 / Biso mean: 33.67 Å2 / Biso min: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2--0.06 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.08→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 43 156 2527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192461
X-RAY DIFFRACTIONr_bond_other_d0.0010.022369
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9543343
X-RAY DIFFRACTIONr_angle_other_deg0.7235470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37724.58396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75115430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.776157
X-RAY DIFFRACTIONr_chiral_restr0.0750.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
X-RAY DIFFRACTIONr_mcbond_it1.6743.2231213
X-RAY DIFFRACTIONr_mcbond_other1.6743.2241214
X-RAY DIFFRACTIONr_mcangle_it2.5244.8141515
LS refinement shellResolution: 2.078→2.132 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 64 -
Rwork0.246 1878 -
all-1942 -
obs--99.79 %

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