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- PDB-6sq3: Crystal structure of mouse PRMT6 in complex with inhibitor U1 -

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Basic information

Entry
Database: PDB / ID: 6sq3
TitleCrystal structure of mouse PRMT6 in complex with inhibitor U1
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-6RE / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.1Jan 24, 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

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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)86,2894
Polymers85,6432
Non-polymers6472
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-33 kcal/mol
Surface area26810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.526, 117.979, 71.945
Angle α, β, γ (deg.)90.000, 103.300, 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-6RE / [[2-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethylamino]-azanyl-methylidene]azanium


Mass: 323.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: PEG 3,350 20%, CH3COONa 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 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.15→45.11 Å / Num. obs: 36561 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 34.46 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.049 / Rrim(I) all: 0.101 / Net I/σ(I): 10.4
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 1 / Num. unique obs: 3146 / CC1/2: 0.294 / Rpim(I) all: 0.766 / Rrim(I) all: 1.166 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4c03

4c03


Resolution: 2.15→29.174 Å / Cross valid method: THROUGHOUT / σ(F): 1.35
RfactorNum. reflection% reflectionSelection details
Rfree0.2955 1824 5 %Random Selection
Rwork0.2507 ---
obs0.2528 36489 99.66 %-
Displacement parametersBiso max: 105.73 Å2 / Biso mean: 45.8698 Å2 / Biso min: 12.93 Å2
Refinement stepCycle: final / Resolution: 2.15→29.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5029 0 46 10 5085
Biso mean--72.75 23.28 -
Num. residues----641
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)
10.24630.2155-0.14981.1584-0.13550.2156-0.0225-0.03120.0055-0.2158-0.01650.0870.09850.04140.04310.28050.0279-0.02620.2660.01680.238931.462616.418382.4697
20.43850.483-0.46771.192-0.56690.79760.0667-0.06080.0310.0244-0.060.1425-0.07980.0249-0.00090.2420.0211-0.02090.2986-0.01620.297924.60612.5499118.4552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 53 through 376)A53 - 376
2X-RAY DIFFRACTION2(chain 'B' and resid 54 through 376)B54 - 376

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