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- PDB-6p7i: Crystal structure of Human PRMT6 in complex with S-Adenosyl-L-Hom... -

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Basic information

Entry
Database: PDB / ID: 6p7i
TitleCrystal structure of Human PRMT6 in complex with S-Adenosyl-L-Homocysteine and YS17-117 Compound
ComponentsProtein arginine N-methyltransferase 6
KeywordsTransferase/Transferase Inhibitor / Protein arginine methyltransferase / PRMT6 / HRMT1L6 / PRMT inhibitors / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity ...histone H2AR3 methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone H3 methyltransferase activity / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / base-excision repair / protein modification process / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / cellular senescence / histone binding / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-O3P / Chem-O3S / S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsHalabelian, L. / Dong, A. / Zeng, H. / Li, Y. / Seitova, A. / Hutchinson, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of a First-in-Class Protein Arginine Methyltransferase 6 (PRMT6) Covalent Inhibitor
Authors: Shen, Y. / Li, F. / Szewczyk, M.M. / Halabelian, L. / Park, K.S. / Chau, I. / Dong, A. / Zeng, H. / Chen, H. / Meng, F. / Barsyte-Lovejoy, D. / Arrowsmith, C.H. / Brown, P.J. / Liu, J. / Vedadi, M. / Jin, J.
History
DepositionJun 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / refine_hist
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.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 6
B: Protein arginine N-methyltransferase 6
C: Protein arginine N-methyltransferase 6
D: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,21614
Polymers168,2984
Non-polymers2,91710
Water13,673759
1
A: Protein arginine N-methyltransferase 6
D: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6097
Polymers84,1492
Non-polymers1,4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-30 kcal/mol
Surface area27710 Å2
MethodPISA
2
B: Protein arginine N-methyltransferase 6
C: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6077
Polymers84,1492
Non-polymers1,4585
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-29 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.091, 135.133, 83.206
Angle α, β, γ (deg.)90.000, 98.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Protein arginine N-methyltransferase 6 / Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 6 / Histone-arginine N- ...Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 6 / Histone-arginine N-methyltransferase PRMT6


Mass: 42074.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT6, HRMT1L6 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q96LA8, type I protein arginine methyltransferase

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Non-polymers , 5 types, 769 molecules

#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-O3P / N-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]prop-2-enamide


Mass: 298.383 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H22N4O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-O3S / N-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]propanamide


Mass: 300.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H24N4O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 759 / 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: 2.58 Å3/Da / Density % sol: 52.38 % / Mosaicity: 0.824 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Sodium Malonate pH 7.0, 12% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 114589 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 1.56 / Net I/σ(I): 9.8 / Num. measured all: 796631
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.035.90.92756000.7180.4091.0160.90398
2.03-2.076.40.72657240.8150.3080.790.85299.8
2.07-2.116.70.61357230.8590.2560.6660.818100
2.11-2.156.80.51356640.8990.2120.5560.85100
2.15-2.26.80.43157450.9210.1780.4670.873100
2.2-2.256.80.36957360.9420.1520.40.912100
2.25-2.316.90.34157120.9530.140.3690.932100
2.31-2.376.90.28157630.9680.1150.3040.988100
2.37-2.446.90.26557030.9740.1080.2861.014100
2.44-2.5270.22957480.9770.0930.2481.088100
2.52-2.6170.19456850.9820.0790.2091.121100
2.61-2.7170.16357250.9890.0660.1761.327100
2.71-2.847.10.13857340.9910.0560.1491.469100
2.84-2.997.20.12157420.9930.0490.1311.728100
2.99-3.177.20.09757390.9950.0390.1052.126100
3.17-3.427.20.08357300.9960.0330.0892.672100
3.42-3.767.30.0757660.9970.0280.0753.054100
3.76-4.317.30.06157490.9980.0240.0652.922100
4.31-5.437.40.05257600.9980.0210.0562.626100
5.43-507.20.04358410.9990.0170.0462.23399.5

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
HKL-3000data reduction
HKL-3000data collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5EGS

5egs


Resolution: 2→32.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.809 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1576 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.145
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 2659 2.3 %RANDOM
Rwork0.1842 ---
obs0.1851 111464 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.66 Å2 / Biso mean: 35.12 Å2 / Biso min: 18.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å21.1 Å2
2---0.63 Å20 Å2
3---0.67 Å2
Refinement stepCycle: final / Resolution: 2→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10574 0 200 767 11541
Biso mean--31.04 41.72 -
Num. residues----1351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911125
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210220
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.96315091
X-RAY DIFFRACTIONr_angle_other_deg0.927323559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03551364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03623.002503
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32151802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.70215101
X-RAY DIFFRACTIONr_chiral_restr0.0810.21643
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022406
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 194 -
Rwork0.297 7687 -
all-7881 -
obs--93.32 %

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