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- PDB-4c04: Crystal structure of M. musculus protein arginine methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 4c04
TitleCrystal structure of M. musculus protein arginine methyltransferase PRMT6 with inhibitor
ComponentsPROTEIN ARGININE N-METHYLTRANSFERASE 6
KeywordsTRANSFERASE
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
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
SINEFUNGIN / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.576 Å
AuthorsBonnefond, L. / Cura, V. / Troffer-Charlier, N. / Mailliot, J. / Wurtz, J.M. / Cavarelli, J.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Functional Insights from High Resolution Structures of Mouse Protein Arginine Methyltransferase 6.
Authors: Bonnefond, L. / Stojko, J. / Mailliot, J. / Troffer-Charlier, N. / Cura, V. / Wurtz, J.M. / Cianferani, S. / Cavarelli, J.
History
DepositionJul 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: 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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN ARGININE N-METHYLTRANSFERASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7032
Polymers42,3221
Non-polymers3811
Water4,035224
1
A: PROTEIN ARGININE N-METHYLTRANSFERASE 6
hetero molecules

A: PROTEIN ARGININE N-METHYLTRANSFERASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4064
Polymers84,6442
Non-polymers7632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area4730 Å2
ΔGint-40.9 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.835, 78.835, 118.472
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 N-METHYLTRANSFERASE 6 / HISTONE-ARGININE N-METHYLTRANSFERASE PRMT6 /


Mass: 42321.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
References: UniProt: Q6NZB1, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.64 % / Description: NONE
Crystal growpH: 7 / Details: 100 MM HEPES PH 7.0, 200 MM MGCL2, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.58→33.79 Å / Num. obs: 49529 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.84
Reflection shellResolution: 1.58→1.63 Å / Redundancy: 5 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.77 / % possible all: 96.6

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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 2Y1W

2y1w


Resolution: 1.576→33.792 Å / SU ML: 0.19 / σ(F): 1.37 / Phase error: 19.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1853 2478 5 %
Rwork0.151 --
obs0.1527 49522 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.576→33.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 27 224 2822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012714
X-RAY DIFFRACTIONf_angle_d1.3213702
X-RAY DIFFRACTIONf_dihedral_angle_d15.2461001
X-RAY DIFFRACTIONf_chiral_restr0.05412
X-RAY DIFFRACTIONf_plane_restr0.007475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5762-1.60660.31481330.27592455X-RAY DIFFRACTION94
1.6066-1.63940.31171370.24052620X-RAY DIFFRACTION100
1.6394-1.6750.2731380.22312622X-RAY DIFFRACTION100
1.675-1.7140.27671380.2092610X-RAY DIFFRACTION100
1.714-1.75680.22471370.19582623X-RAY DIFFRACTION100
1.7568-1.80430.23781370.18252603X-RAY DIFFRACTION100
1.8043-1.85740.22361400.17622624X-RAY DIFFRACTION100
1.8574-1.91740.19851340.17042621X-RAY DIFFRACTION100
1.9174-1.98590.20771400.15752610X-RAY DIFFRACTION100
1.9859-2.06540.18731400.15332626X-RAY DIFFRACTION100
2.0654-2.15940.18961370.14672602X-RAY DIFFRACTION100
2.1594-2.27320.17061350.14012618X-RAY DIFFRACTION100
2.2732-2.41560.15941380.13592629X-RAY DIFFRACTION100
2.4156-2.6020.18631390.14512628X-RAY DIFFRACTION100
2.602-2.86370.17261390.14772619X-RAY DIFFRACTION100
2.8637-3.27780.19081370.15262655X-RAY DIFFRACTION100
3.2778-4.12860.16211400.13352615X-RAY DIFFRACTION100
4.1286-33.79930.17031390.13942664X-RAY DIFFRACTION100
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)
12.423-2.5228-4.1753.01064.90968.04120.402-0.1371-0.04811.2589-0.381-0.1-2.01770.2938-0.03020.8419-0.01850.00330.6681-0.00050.451541.0643-18.8291-0.8727
22.5567-0.5270.90541.99920.27463.28330.14720.0913-0.28630.0301-0.04150.09590.1825-0.0411-0.08580.14550.00280.01350.1671-0.00440.198417.0734-17.79217.5105
32.34312.59261.2414.71662.05591.74360.03320.1196-0.0652-0.1091-0.09320.21230.0023-0.09090.06950.14110.0475-0.00570.19860.00380.170311.9845-4.4553.9741
47.19872.67543.51190.50011.06391.16810.06340.23880.14190.07460.00850.05040.00910.0707-0.06950.2210.01990.01450.3398-0.0030.253244.045818.729611.8138
53.1809-0.06012.0376.97542.26247.5476-0.0089-0.38640.19640.3146-0.0806-0.0167-0.04690.03350.05680.164-0.03120.05660.06160.05610.081321.412911.738416.0002
61.74070.6698-0.16072.61330.12571.27250.04390.02640.16350.1092-0.01670.1632-0.1106-0.042-0.02060.13530.01880.03440.15530.01480.125918.526311.018711.9899
73.58490.93010.50082.5112.11657.98890.15870.29420.1182-0.4298-0.18680.0208-0.2569-0.16230.0070.15570.01010.04350.21450.08340.180421.512716.28510.634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 48:54)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 55:147)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 148:201)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 202:240)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 241:258)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 259:342)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 343:376)

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