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- PDB-6sqi: Crystal structure of mouse PRMT6 with C-terminal TEV cleavage site -

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Basic information

Entry
Database: PDB / ID: 6sqi
TitleCrystal structure of mouse PRMT6 with 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 / protein-arginine omega-N monomethyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase / histone H4R3 methyltransferase activity / : / protein-arginine N-methyltransferase activity ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase / histone H4R3 methyltransferase activity / : / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / 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 / methylation / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
: / Arginine methyltransferase oligomerization subdomain / 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: 1.6 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8612
Polymers42,8211
Non-polymers401
Water3,945219
1
A: Protein arginine N-methyltransferase 6
hetero molecules

A: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7234
Polymers85,6432
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area3610 Å2
ΔGint-58 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.644, 79.644, 117.738
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

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


Mass: 42821.301 Da / Num. of mol.: 1 / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.79 % / Mosaicity: 0.11 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: PEG Smear High 8%, NaCHOO 40 mM, CaCl2 40 mM, PIPES pH 6.8 100 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: Sep 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.16
ReflectionResolution: 1.6→40.69 Å / Num. obs: 47624 / % possible obs: 99 % / Redundancy: 8.6 % / Biso Wilson estimate: 19.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.016 / Rrim(I) all: 0.052 / Net I/σ(I): 22.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2048 / CC1/2: 0.436 / Rpim(I) all: 0.529 / Rrim(I) all: 0.913 / % possible all: 85.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13rc2_2975refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c03

4c03


Resolution: 1.6→40.69 Å / Cross valid method: THROUGHOUT / σ(F): 1.33
RfactorNum. reflection% reflection
Rfree0.1673 2389 5.02 %
Rwork0.1441 --
obs0.1474 47599 99.04 %
Displacement parametersBiso max: 97.84 Å2 / Biso mean: 26.7729 Å2 / Biso min: 12.21 Å2
Refinement stepCycle: final / Resolution: 1.6→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 1 219 2849
Biso mean--16.81 31.88 -
Num. residues----335
Refinement TLS params.Method: refined / Origin x: 21.2622 Å / Origin y: 1.4764 Å / Origin z: 8.3403 Å
111213212223313233
T0.1738 Å20.0049 Å20.0202 Å2-0.1732 Å20.0063 Å2--0.1193 Å2
L0.4418 °20.2147 °2-0.006 °2-0.4952 °20.048 °2--0.2462 °2
S0.0186 Å °-0.0184 Å °0.0243 Å °0.0071 Å °-0.0049 Å °0.0331 Å °-0.01 Å °-0.0049 Å °-0.0194 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 52 through 386)

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