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- PDB-5fqn: Crystal structure of M. musculus protein arginine methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 5fqn
TitleCrystal structure of M. musculus protein arginine methyltransferase PRMT6 with SAH at 1.65 Angstroms
ComponentsPROTEIN ARGININE METHYLTRANSFERASE 6
KeywordsTRANSFERASE / S-ADENOSYL-L-METHIONINE
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 / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase 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 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 methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / protein modification process / cellular senescence / methylation / 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
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
S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.657 Å
AuthorsBonnefond, L. / Cavarelli, J.
CitationJournal: To be Published
Title: Crystal Strcutures of Prmt6 in Complex with Sah in Alternative Conformations
Authors: Bonnefond, L. / Cura, V. / Troffer-Charlier, N. / Cavarelli, J.
History
DepositionDec 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: PROTEIN ARGININE METHYLTRANSFERASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7402
Polymers44,3561
Non-polymers3841
Water3,207178
1
A: PROTEIN ARGININE METHYLTRANSFERASE 6
hetero molecules

A: PROTEIN ARGININE METHYLTRANSFERASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4814
Polymers88,7122
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area4170 Å2
ΔGint-42 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.426, 79.426, 118.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein PROTEIN ARGININE METHYLTRANSFERASE 6


Mass: 44355.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PNEA-VH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6NZB1, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsL315P NATURAL VARIANT

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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: 2.11 Å3/Da / Density % sol: 41.65 % / Description: NONE
Crystal growpH: 8 / Details: 100 MM TRIS PH 8.0 200 MM MGCL2 12% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2015
Details: A CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK- BAEZ PAIR OF FOCUSSING MIRRORS
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL CUT CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.65→40.8 Å / Num. obs: 43482 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 23.97 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.1
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.724 / Mean I/σ(I) obs: 0.8 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C08

4c08


Resolution: 1.657→40.772 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 23.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 2172 5 %
Rwork0.1776 --
obs0.1793 43482 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.2 Å2
Refinement stepCycle: LAST / Resolution: 1.657→40.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 26 178 2735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132688
X-RAY DIFFRACTIONf_angle_d1.353655
X-RAY DIFFRACTIONf_dihedral_angle_d13.8681602
X-RAY DIFFRACTIONf_chiral_restr0.084406
X-RAY DIFFRACTIONf_plane_restr0.009465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6567-1.69280.30381340.3162555X-RAY DIFFRACTION99
1.6928-1.73210.30881360.30372583X-RAY DIFFRACTION100
1.7321-1.77540.32941360.26562589X-RAY DIFFRACTION100
1.7754-1.82350.27861350.25252566X-RAY DIFFRACTION100
1.8235-1.87710.25921360.22762586X-RAY DIFFRACTION100
1.8771-1.93770.23151350.21022569X-RAY DIFFRACTION100
1.9377-2.00690.1951360.19472568X-RAY DIFFRACTION100
2.0069-2.08730.21941350.17782573X-RAY DIFFRACTION100
2.0873-2.18230.23171350.18392559X-RAY DIFFRACTION100
2.1823-2.29730.22161360.17382597X-RAY DIFFRACTION100
2.2973-2.44130.22521360.17742580X-RAY DIFFRACTION100
2.4413-2.62970.19831370.1732602X-RAY DIFFRACTION100
2.6297-2.89430.21971350.18462585X-RAY DIFFRACTION100
2.8943-3.31290.24141360.18142589X-RAY DIFFRACTION100
3.3129-4.17330.191360.15172581X-RAY DIFFRACTION100
4.1733-40.7840.16541380.14752628X-RAY DIFFRACTION100

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