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- PDB-6sqh: Crystal structure of mouse PRMT6 with partial C-terminal TEV clea... -

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Basic information

Entry
Database: PDB / ID: 6sqh
TitleCrystal structure of mouse PRMT6 with partial C-terminal TEV cleavage site
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
Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39 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 4, 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


Theoretical massNumber of molelcules
Total (without water)85,6432
Polymers85,6432
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-40 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.143, 118.106, 71.760
Angle α, β, γ (deg.)90.000, 103.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein arginine N-methyltransferase 6


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

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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: 2.36 Å3/Da / Density % sol: 47.86 % / Mosaicity: 0.28 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: PEG Smear Broad 22%, MES pH 6.5 100 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 EIGER X 4M / Detector: PIXEL / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.39→45.1 Å / Num. obs: 26129 / % possible obs: 98.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 31.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.056 / Rrim(I) all: 0.117 / Net I/σ(I): 13.1
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2 / Num. unique obs: 2472 / CC1/2: 0.782 / Rpim(I) all: 0.396 / Rrim(I) all: 0.8 / % possible all: 89.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3546refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c03

4c03


Resolution: 2.39→36.851 Å / Cross valid method: THROUGHOUT / σ(F): 1.35
RfactorNum. reflection% reflection
Rfree0.2683 1300 4.98 %
Rwork0.2088 --
obs0.2116 26098 98.78 %
Displacement parametersBiso max: 85.8 Å2 / Biso mean: 31.1453 Å2 / Biso min: 8.08 Å2
Refinement stepCycle: final / Resolution: 2.39→36.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5059 0 23 0 5082
Biso mean--37.62 --
Num. residues----643
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)
10.50940.0688-0.24940.4943-0.28730.67980.05710.04140.0949-0.0593-0.0350.0864-0.12370.0539-0.0950.09710.00920.01050.0668-0.00920.07317.764310.077513.2246
20.26390.0325-0.07110.70910.16380.7221-0.0542-0.0563-0.0164-0.0869-0.00960.12610.10320.0477-0.00460.17330.0112-0.0080.1961-0.00380.171214.916914.1071-22.7152
30.0324-0.031-0.07170.04590.07870.1736-0.0719-0.02120.0104-0.0035-0.0001-0.017-0.0349-0.0251-0.00090.23180.11030.10970.47070.0140.410930.179222.4139-7.7479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 52 through 376)A52 - 376
2X-RAY DIFFRACTION2(chain 'B' and resid 53 through 376)B53 - 376
3X-RAY DIFFRACTION3(chain 'A' and resid 384 through 385)A384 - 385

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