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- PDB-8g2f: Crystal Structure of PRMT3 with Compound II710 -

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Basic information

Entry
Database: PDB / ID: 8g2f
TitleCrystal Structure of PRMT3 with Compound II710
ComponentsProtein arginine N-methyltransferase 3
KeywordsTRANSFERASE/INHIBITOR / PRMT3 / II710 / TRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium / SGC / 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) / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-DVS / Protein arginine N-methyltransferase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsSong, X. / Dong, A. / Deng, Y. / Huang, R. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: Acta Pharm Sin B / Year: 2023
Title: A unique binding pocket induced by a noncanonical SAH mimic to develop potent and selective PRMT inhibitors.
Authors: Deng, Y. / Song, X. / Iyamu, I.D. / Dong, A. / Min, J. / Huang, R.
History
DepositionFeb 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7542
Polymers38,2821
Non-polymers4731
Water75742
1
A: Protein arginine N-methyltransferase 3
hetero molecules

A: Protein arginine N-methyltransferase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5094
Polymers76,5642
Non-polymers9452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3290 Å2
ΔGint-32 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.733, 70.733, 175.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThis construct only comprises the methyltransferase domain of Protein arginine N-methyltransferase 3. The authors do not know the quaternary structure of this domain in isolation. However, the software PISA predicts it to be a dimer.

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Components

#1: Protein Protein arginine N-methyltransferase 3 / Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 3


Mass: 38281.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT3, HRMT1L3 / Production host: Escherichia coli (E. coli)
References: UniProt: O60678, type I protein arginine methyltransferase
#2: Chemical ChemComp-DVS / 5'-S-[3-(N'-benzylcarbamimidamido)propyl]-5'-thioadenosine


Mass: 472.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N8O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.3 M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 27517 / % possible obs: 97.4 % / Redundancy: 10.4 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.09 / Χ2: 1.823 / Net I/av σ(I): 30.9 / Net I/σ(I): 8.9
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1125 / CC1/2: 0.915 / CC star: 0.978 / Χ2: 0.798 / % possible all: 81.6

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0258refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→48.14 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.957 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25598 1088 4 %RANDOM
Rwork0.20695 ---
obs0.20883 26354 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.369 Å2
Baniso -1Baniso -2Baniso -3
1-3.09 Å2-0 Å2-0 Å2
2--3.09 Å2-0 Å2
3----6.17 Å2
Refinement stepCycle: 1 / Resolution: 2.06→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 33 42 2413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132443
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172245
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.6313316
X-RAY DIFFRACTIONr_angle_other_deg1.2431.5845201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5255305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74623.762101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66415411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.539156
X-RAY DIFFRACTIONr_chiral_restr0.0570.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022789
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02493
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_it4.2335.7591220
X-RAY DIFFRACTIONr_mcbond_other4.2335.7551219
X-RAY DIFFRACTIONr_mcangle_it5.4198.621525
X-RAY DIFFRACTIONr_mcangle_other5.4198.6231526
X-RAY DIFFRACTIONr_scbond_it4.7966.1041223
X-RAY DIFFRACTIONr_scbond_other4.7946.1041224
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4649.0151792
X-RAY DIFFRACTIONr_long_range_B_refined7.71267.1932595
X-RAY DIFFRACTIONr_long_range_B_other7.71867.1872588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.064→2.117 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 69 -
Rwork0.368 1513 -
obs--77.66 %

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