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- PDB-5egs: Human PRMT6 with bound fragment-type inhibitor -

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Basic information

Entry
Database: PDB / ID: 5egs
TitleHuman PRMT6 with bound fragment-type inhibitor
ComponentsProtein arginine N-methyltransferase 6
KeywordsTRANSFERASE / Fragment / Inhibitor / PRMT
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4R3 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone H2AQ104 methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / base-excision repair / protein modification process / RMTs methylate histone arginines / cellular senescence / methylation / histone binding / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich ...Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / 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
2-[4-(phenylmethyl)piperidin-1-yl]ethanamine / S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSteuber, H. / Egner, U. / Kania, J. / Wu, H. / Brown, P.J.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery of a Potent Class I Protein Arginine Methyltransferase Fragment Inhibitor.
Authors: Ferreira de Freitas, R. / Eram, M.S. / Szewczyk, M.M. / Steuber, H. / Smil, D. / Wu, H. / Li, F. / Senisterra, G. / Dong, A. / Brown, P.J. / Hitchcock, M. / Moosmayer, D. / Stegmann, C.M. / ...Authors: Ferreira de Freitas, R. / Eram, M.S. / Szewczyk, M.M. / Steuber, H. / Smil, D. / Wu, H. / Li, F. / Senisterra, G. / Dong, A. / Brown, P.J. / Hitchcock, M. / Moosmayer, D. / Stegmann, C.M. / Egner, U. / Arrowsmith, C. / Barsyte-Lovejoy, D. / Vedadi, M. / Schapira, M.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
C: Protein arginine N-methyltransferase 6
D: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,14614
Polymers168,2984
Non-polymers2,84810
Water7,296405
1
A: Protein arginine N-methyltransferase 6
D: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5737
Polymers84,1492
Non-polymers1,4245
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-28 kcal/mol
Surface area28000 Å2
MethodPISA
2
B: Protein arginine N-methyltransferase 6
C: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5737
Polymers84,1492
Non-polymers1,4245
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-28 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.157, 135.616, 83.086
Angle α, β, γ (deg.)90.00, 98.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q96LA8, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Chemical
ChemComp-SAH / 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-5NR / 2-[4-(phenylmethyl)piperidin-1-yl]ethanamine


Mass: 218.338 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H22N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25 % PEG 1500; 0.1 M MMT pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 90370 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 8.4
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 1.7 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HC4

4hc4


Resolution: 2.15→41.26 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 13.831 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24648 2101 2.3 %RANDOM
Rwork0.20065 ---
obs0.20174 88269 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.752 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å20.56 Å2
2---0.12 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10633 0 200 405 11238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01911108
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210542
X-RAY DIFFRACTIONr_angle_refined_deg2.1341.97315046
X-RAY DIFFRACTIONr_angle_other_deg1.1433.00224023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47451344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4523.078523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.988151839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.88215103
X-RAY DIFFRACTIONr_chiral_restr0.1250.21635
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212471
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022614
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_it0.851.3355388
X-RAY DIFFRACTIONr_mcbond_other0.851.3345387
X-RAY DIFFRACTIONr_mcangle_it1.4621.9936719
X-RAY DIFFRACTIONr_mcangle_other1.4621.9936720
X-RAY DIFFRACTIONr_scbond_it1.0611.5145720
X-RAY DIFFRACTIONr_scbond_other1.0611.5145721
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7772.2168325
X-RAY DIFFRACTIONr_long_range_B_refined4.45511.24312513
X-RAY DIFFRACTIONr_long_range_B_other4.45511.24612514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.154→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 146 -
Rwork0.295 6132 -
obs--93.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.99280.1531-0.38321.0642-0.26951.04690.02650.038-0.06790.0693-0.0201-0.10980.09470.0424-0.00640.224-0.0150.05390.0103-0.01410.04527.4097-23.502411.0418
22.4752-0.67490.05241.2476-0.08110.622-0.0251-0.04010.00470.0799-0.02160.13310.066-0.12770.04670.1688-0.03420.06990.0305-0.02180.0409-18.065-5.822138.5732
32.3063-0.30020.84571.1558-0.1731.0172-0.0241-0.04930.15770.043-0.029-0.2092-0.1550.0220.05310.2-0.01350.06780.0061-0.00510.08772.995424.141932.1417
41.95440.46940.48591.70830.17580.9934-0.050.055-0.009-0.03860.0310.1438-0.0977-0.20720.01890.24950.040.09170.05980.00540.0517-12.42014.7617-1.816
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 375
2X-RAY DIFFRACTION2B38 - 375
3X-RAY DIFFRACTION3C39 - 375
4X-RAY DIFFRACTION4D38 - 375

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