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- PDB-4c05: Crystal structure of M. musculus protein arginine methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 4c05
TitleCrystal structure of M. musculus protein arginine methyltransferase PRMT6 with SAH
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 / 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: 2.195 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 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Dec 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

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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)42,7062
Polymers42,3221
Non-polymers3841
Water1,31573
1
A: PROTEIN ARGININE N-METHYLTRANSFERASE 6
hetero molecules

A: PROTEIN ARGININE N-METHYLTRANSFERASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4124
Polymers84,6442
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area3250 Å2
ΔGint-33.9 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.427, 78.427, 118.126
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / 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.: 73 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.09 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

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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
Reflection twinOperator: h,-k,-l / Fraction: 0.73
ReflectionResolution: 2.2→40.43 Å / Num. obs: 17706 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 4.08 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.46
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.37 / % possible all: 78.6

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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: 2.195→40.428 Å / σ(F): 1.98 / Phase error: 21.07 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.185 900 5.1 %
Rwork0.1462 --
obs0.1681 17706 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.195→40.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 26 73 2592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092590
X-RAY DIFFRACTIONf_angle_d1.0433519
X-RAY DIFFRACTIONf_dihedral_angle_d16.13956
X-RAY DIFFRACTIONf_chiral_restr0.048390
X-RAY DIFFRACTIONf_plane_restr0.004453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1983-2.3360.27621310.2312426X-RAY DIFFRACTION80
2.336-2.51630.24591500.20422871X-RAY DIFFRACTION94
2.5163-2.76940.20411500.18962844X-RAY DIFFRACTION95
2.7694-3.16990.21321490.17292871X-RAY DIFFRACTION95
3.1699-3.99290.21141540.16492884X-RAY DIFFRACTION95
3.9929-35.19380.17511520.13852906X-RAY DIFFRACTION95
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)
13.5664-0.53420.34973.02330.54265.10550.10020.0349-0.29250.0654-0.03610.12320.1113-0.11-0.06170.19850.010.01040.19350.00990.153416.693-17.68667.5232
23.64984.28341.69347.68192.75121.91620.05530.2967-0.0983-0.058-0.04980.120.0233-0.08420.01380.2080.0604-0.01680.2870.02370.11511.8741-4.3773.9426
38.55633.64974.09311.61261.78541.92930.15170.0793-0.03380.1886-0.05390.00110.17060.1602-0.08840.28420.00790.020.32290.00020.209543.522618.215111.9864
43.4373-0.18710.51845.40252.83033.58920.0942-0.16940.14550.4703-0.0730.0002-0.0708-0.02650.00260.3156-0.0180.06250.18440.09060.094220.755111.862816.4144
52.30771.99220.13113.83150.57541.2450.03520.13280.1020.1433-0.01710.1268-0.0941-0.0881-0.01450.20960.04360.03430.22370.04170.113618.278110.740612.0592
65.78570.93020.49173.44955.14559.06320.03880.28380.1982-0.632-0.05220.1833-0.3289-0.15770.01650.2409-0.02170.0420.27150.08480.144621.510316.31860.6002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 56:147)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 148:201)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 202:240)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 241:258)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 259:342)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 343:376)

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