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- PDB-5e8r: Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae) -

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Basic information

Entry
Database: PDB / ID: 5e8r
TitleHuman HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae)
ComponentsProtein arginine N-methyltransferase 6
KeywordsTRANSFERASE / HRMT1L6 / MS-023 / Structural Genomics / Structural Genomics Consortium / SGC
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. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / 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-5L6 / S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.55 Å
AuthorsDONG, A. / ZENG, H. / LIU, J. / TEMPEL, W. / Seitova, A. / Hutchinson, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / JIN, J. ...DONG, A. / ZENG, H. / LIU, J. / TEMPEL, W. / Seitova, A. / Hutchinson, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / JIN, J. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: A Potent, Selective, and Cell-Active Inhibitor of Human Type I Protein Arginine Methyltransferases.
Authors: Eram, M.S. / Shen, Y. / Szewczyk, M.M. / Wu, H. / Senisterra, G. / Li, F. / Butler, K.V. / Kaniskan, H.U. / Speed, B.A. / Dela Sena, C. / Dong, A. / Zeng, H. / Schapira, M. / Brown, P.J. / ...Authors: Eram, M.S. / Shen, Y. / Szewczyk, M.M. / Wu, H. / Senisterra, G. / Li, F. / Butler, K.V. / Kaniskan, H.U. / Speed, B.A. / Dela Sena, C. / Dong, A. / Zeng, H. / Schapira, M. / Brown, P.J. / Arrowsmith, C.H. / Barsyte-Lovejoy, D. / Liu, J. / Vedadi, M. / Jin, J.
History
DepositionOct 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jan 24, 2018Group: Derived calculations / Structure summary / Category: audit_author / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,67020
Polymers84,1492
Non-polymers1,52118
Water1,17165
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-89 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.244, 100.244, 89.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
DetailsAs per the authors the biological assembly is unknown

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
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) / Strain (production host): Sf9
References: UniProt: Q96LA8, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125

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Non-polymers , 5 types, 83 molecules

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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-5L6 / N-methyl-N-({4-[4-(propan-2-yloxy)phenyl]-1H-pyrrol-3-yl}methyl)ethane-1,2-diamine


Mass: 287.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H25N3O
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Num. of mol.: 9 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 10% PEG 3350, 0.2M MgCl2, 0.1M Sodium Cacadylate, pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 28929 / % possible obs: 99.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.116 / Rrim(I) all: 0.198 / Χ2: 1.693 / Net I/av σ(I): 8.89 / Net I/σ(I): 6.5 / Num. measured all: 91551
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.55-2.593.20.89314360.3870.6061.092100
2.59-2.643.20.76514780.5180.5171.1121000.927
2.64-2.693.20.6314060.5670.4311.1391000.766
2.69-2.753.20.59814790.5670.4071.1531000.726
2.75-2.813.20.54114520.660.3661.161000.656
2.81-2.873.20.44814410.7220.3021.2081000.543
2.87-2.943.20.40114490.7530.2731.18199.90.487
2.94-3.023.20.32914430.8290.2221.30799.70.399
3.02-3.113.20.26314410.8760.1771.3091000.318
3.11-3.213.20.22614450.9080.1531.4081000.274
3.21-3.333.20.19414570.9380.131.56299.90.235
3.33-3.463.20.16814610.9490.1141.60799.90.204
3.46-3.623.20.15114300.9610.1021.70399.80.183
3.62-3.813.20.12614480.940.0842.15899.50.152
3.81-4.053.20.10514460.9050.0711.92599.50.127
4.05-4.363.10.09514600.9780.0642.69699.30.115
4.36-4.830.0914300.9820.0613.26697.80.109
4.8-5.493.10.08814340.9840.0593.35198.60.106
5.49-6.923.20.07514380.9880.051.90397.70.09
6.92-503.20.04114550.9970.0271.90295.40.049

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementResolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.875 / WRfactor Rfree: 0.2218 / WRfactor Rwork: 0.1778 / FOM work R set: 0.7859 / SU B: 11.493 / SU ML: 0.247 / SU R Cruickshank DPI: 0.4657 / SU Rfree: 0.2787 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.499 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 870 3 %RANDOM
Rwork0.2201 ---
obs0.2213 28018 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.11 Å2 / Biso mean: 25.338 Å2 / Biso min: 9.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--0.62 Å20 Å2
3----1.24 Å2
Refinement stepCycle: final / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5062 0 108 65 5235
Biso mean--26.71 18.94 -
Num. residues----665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195349
X-RAY DIFFRACTIONr_bond_other_d0.0010.025018
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.9637281
X-RAY DIFFRACTIONr_angle_other_deg0.854311461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5285679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14622.661218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52715826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1361544
X-RAY DIFFRACTIONr_chiral_restr0.0610.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216205
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021273
X-RAY DIFFRACTIONr_mcbond_it0.8872.6132692
X-RAY DIFFRACTIONr_mcbond_other0.8872.6132693
X-RAY DIFFRACTIONr_mcangle_it1.6063.9133366
LS refinement shellResolution: 2.551→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 61 -
Rwork0.299 2071 -
all-2132 -
obs--99.86 %

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