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- PDB-4x41: Crystal Structure of Protein Arginine Methyltransferase PRMT8 -

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Basic information

Entry
Database: PDB / ID: 4x41
TitleCrystal Structure of Protein Arginine Methyltransferase PRMT8
ComponentsProtein arginine N-methyltransferase 8
KeywordsTRANSFERASE / protein arginine methyltransferase / methylation / dimerization
Function / homology
Function and homology information


protein-arginine omega-N monomethyltransferase activity / histone H4 methyltransferase activity / peptidyl-arginine methylation / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of protein binding / protein methylation / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / protein homooligomerization ...protein-arginine omega-N monomethyltransferase activity / histone H4 methyltransferase activity / peptidyl-arginine methylation / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of protein binding / protein methylation / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / protein homooligomerization / cytoplasmic side of plasma membrane / enzyme binding / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / 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 ...Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / 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 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsLee, W.C. / Ho, M.C.
CitationJournal: Biochemistry / Year: 2015
Title: Protein Arginine Methyltransferase 8: Tetrameric Structure and Protein Substrate Specificity
Authors: Lee, W.C. / Lin, W.L. / Matsui, T. / Chen, E.S. / Wei, T.Y. / Lin, W.H. / Hu, H. / Zheng, Y.G. / Tsai, M.D. / Ho, M.C.
History
DepositionDec 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 8
B: Protein arginine N-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6133
Polymers83,2292
Non-polymers3841
Water0
1
A: Protein arginine N-methyltransferase 8
B: Protein arginine N-methyltransferase 8
hetero molecules

A: Protein arginine N-methyltransferase 8
B: Protein arginine N-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,2276
Polymers166,4584
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Unit cell
Length a, b, c (Å)68.159, 78.236, 203.861
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Protein arginine N-methyltransferase 8 / Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 4


Mass: 41614.520 Da / Num. of mol.: 2 / Fragment: UNP residues 52-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT8, HRMT1L3, HRMT1L4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR22, EC: 2.1.1.125
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
Sequence detailsTHIS SEQUENCE IS BASED ON GENBANK AAH22458.2. RESIDUE 141 IS GLU IN AAH22458.2.

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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: 3.27 Å3/Da / Density % sol: 67.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 150mM D-glucose, 100mM HEPES/MOPS pH7.5, 40% Glycerol/PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 13561 / % possible obs: 94.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 58.37 Å2 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.133 / Rrim(I) all: 0.239 / Χ2: 0.995 / Net I/av σ(I): 3.979 / Net I/σ(I): 5.7 / Num. measured all: 38801
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.622.80.47813620.6920.3320.5861.20997.1
3.62-3.772.90.38613630.7950.2640.4711.07996.7
3.77-3.942.80.34313450.8180.2360.4191.10696.5
3.94-4.142.90.26613600.9010.1820.3241.06596
4.14-4.42.90.19413350.9330.130.2350.90895.8
4.4-4.742.90.17813670.9470.1190.2150.94595.6
4.74-5.212.90.1613620.9640.1060.1930.92594.2
5.21-5.942.90.17313310.9540.1140.2091.07594.2
5.94-7.422.90.14913700.9610.0990.180.88192.6
7.42-202.70.06413660.9930.0430.0780.75688.8

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Processing

Software
NameVersionClassification
PHENIXdev_1819refinement
SCALAdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→19.727 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 683 5.04 %
Rwork0.2313 12872 -
obs0.2339 13555 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.04 Å2 / Biso mean: 55.274 Å2 / Biso min: 20.35 Å2
Refinement stepCycle: final / Resolution: 3.5→19.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 26 0 4998
Biso mean--61.31 --
Num. residues----614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055115
X-RAY DIFFRACTIONf_angle_d1.0196919
X-RAY DIFFRACTIONf_chiral_restr0.041770
X-RAY DIFFRACTIONf_plane_restr0.005862
X-RAY DIFFRACTIONf_dihedral_angle_d15.31871
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5002-3.76880.35131400.29442577271797
3.7688-4.14490.31471450.25522564270996
4.1449-4.73740.26571290.21142570269996
4.7374-5.94140.27651190.21342578269794
5.9414-19.72770.23691500.20892583273391

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