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- PDB-6sq4: Crystal structure of mouse PRMT6 in complex with inhibitor U2 -

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Basic information

Entry
Database: PDB / ID: 6sq4
TitleCrystal structure of mouse PRMT6 in complex with inhibitor U2
ComponentsProtein arginine N-methyltransferase 6
KeywordsTRANSFERASE / SAM binding domain / arginine methylation
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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / 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 / protein modification process / cellular senescence / histone binding / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-GJV / IODIDE ION / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.7 Å
AuthorsBonnefond, L. / Cavarelli, J.
CitationJournal: To be published
Title: Crystal structure of mouse PRMT6 in complex with inhibitors
Authors: Bonnefond, L. / Cavarelli, J.
History
DepositionSep 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 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

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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)86,5716
Polymers85,6432
Non-polymers9294
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-33 kcal/mol
Surface area28160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.950, 118.101, 72.093
Angle α, β, γ (deg.)90.000, 103.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein arginine N-methyltransferase 6 / Histone-arginine N-methyltransferase PRMT6


Mass: 42821.301 Da / Num. of mol.: 2 / Fragment: mouse PRMT6 / Mutation: F315L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prmt6, Hrmt1l6 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6NZB1, type I protein arginine methyltransferase
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-GJV / 9-(7-{[amino(iminio)methyl]amino}-5,6,7-trideoxy-beta-D-ribo-heptofuranosyl)-9H-purin-6-amine


Mass: 337.358 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H21N8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.34 Å3/Da / Density % sol: 47.53 % / Mosaicity: 0.2 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 3,350 20%, NaI 200 mM, Tris-HCl pH 7.5 100 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→45.17 Å / Num. obs: 74687 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 20.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.023 / Rrim(I) all: 0.058 / Net I/σ(I): 16.5 / Num. measured all: 361459 / Scaling rejects: 160
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3909 / CC1/2: 0.454 / Rpim(I) all: 0.621 / Rrim(I) all: 1.125 / % possible all: 98.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→35.058 Å / Cross valid method: THROUGHOUT / σ(F): 1.37
RfactorNum. reflection% reflection
Rfree0.2111 3698 4.95 %
Rwork0.1813 --
obs0.1828 74636 99.74 %
Displacement parametersBiso max: 95.61 Å2 / Biso mean: 30.2832 Å2 / Biso min: 11.89 Å2
Refinement stepCycle: final / Resolution: 1.7→35.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5208 0 91 446 5745
Biso mean--25.65 35.21 -
Num. residues----661
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)
10.24590.2171-0.10811.4193-0.09460.3542-0.04480.00020.0227-0.2301-0.01190.04990.06790.02450.05920.15660.0239-0.0180.13630.00050.130331.275116.064282.7618
20.540.6048-0.29911.366-0.6380.36860.06130.01590.07850.1397-0.03830.1193-0.08720.0144-0.02110.17190.00020.0110.1407-0.01430.158924.398911.5128118.493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 41 through 376)A41 - 376
2X-RAY DIFFRACTION2(chain 'B' and resid 47 through 376)B47 - 376

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