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- PDB-4hsg: Crystal structure of human PRMT3 in complex with an allosteric in... -

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Basic information

Entry
Database: PDB / ID: 4hsg
TitleCrystal structure of human PRMT3 in complex with an allosteric inhibitor (PRMT3- KTD)
ComponentsPRMT3 protein
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PRMT3 / allosteric inhibitor / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE-TRANSFERASE INHIBITOR complex
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-KTD / Protein arginine N-methyltransferase 3 / PRMT3 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDobrovetsky, E. / Dong, A. / Liu, F. / Li, F. / Tempel, W. / Siarheyeva, A. / Hajian, T. / Smil, D. / Bountra, C. / Arrowsmith, C.H. ...Dobrovetsky, E. / Dong, A. / Liu, F. / Li, F. / Tempel, W. / Siarheyeva, A. / Hajian, T. / Smil, D. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Schapira, M. / Jin, J. / Vedadi, M. / Structural Genomics Consortium (SGC)
CitationJournal: J. Med. Chem. / Year: 2013
Title: Exploiting an allosteric binding site of PRMT3 yields potent and selective inhibitors.
Authors: Liu, F. / Li, F. / Ma, A. / Dobrovetsky, E. / Dong, A. / Gao, C. / Korboukh, I. / Liu, J. / Smil, D. / Brown, P.J. / Frye, S.V. / Arrowsmith, C.H. / Schapira, M. / Vedadi, M. / Jin, J.
History
DepositionOct 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: 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

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Assembly

Deposited unit
A: PRMT3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,59419
Polymers38,2821
Non-polymers31218
Water2,072115
1
A: PRMT3 protein
hetero molecules

A: PRMT3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,18938
Polymers76,5642
Non-polymers62536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3350 Å2
ΔGint-30 kcal/mol
Surface area25390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.699, 70.699, 172.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: pET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-PRAR2 / References: UniProt: Q8WUV3, UniProt: O60678*PLUS
#2: Chemical ChemComp-KTD / 1-(1,2,3-benzothiadiazol-6-yl)-3-(2-oxo-2-phenylethyl)urea


Mass: 312.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12N4O2S
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 17 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 25% PEG 3350, 0.2 M Lithium Sulfate, 0.1 M Hepes pH7.5, vapor diffusion hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20339 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 25.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.847 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
Coot0.6.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SMQ
Resolution: 2.3→48.07 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 5.513 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.221 838 4.2 %RANDOM
Rwork0.192 ---
obs0.193 20180 99.4 %-
all-20180 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 39 115 2459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192423
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9663295
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5715310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00524.52695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97415420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.458157
X-RAY DIFFRACTIONr_chiral_restr0.0790.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211784
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 55 -
Rwork0.23 1401 -
obs--99.39 %

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