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- PDB-3ua4: Crystal Structure of Protein Arginine Methyltransferase PRMT5 -

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Basic information

Entry
Database: PDB / ID: 3ua4
TitleCrystal Structure of Protein Arginine Methyltransferase PRMT5
ComponentsProtein arginine N-methyltransferase 5
KeywordsTRANSFERASE / TIM-barrel / Rossmann Fold / beta-barrel / symmetric arginine dimethylase / Symmetric dimethylation / nucleus
Function / homology
Function and homology information


histone H2A methyltransferase activity / response to odorant / protein-arginine omega-N monomethyltransferase activity / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / histone arginine N-methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity ...histone H2A methyltransferase activity / response to odorant / protein-arginine omega-N monomethyltransferase activity / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / histone arginine N-methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / histone H4R3 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / protein-arginine N-methyltransferase activity / histone H2A Q104 methyltransferase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / locomotory behavior / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / DNA-binding transcription factor binding / methylation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / nucleus / cytosol
Similarity search - Function
Protein arginine N-methyltransferase PRMT5 / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 arginine-N-methyltransferase / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase ...Protein arginine N-methyltransferase PRMT5 / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 arginine-N-methyltransferase / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Divalent-metal-dependent TIM barrel enzymes / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein arginine N-methyltransferase 5
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.005 Å
AuthorsSun, L. / Wang, M. / Lv, Z. / Yang, N. / Liu, Y. / Bao, S. / Gong, W. / Xu, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural insights into protein arginine symmetric dimethylation by PRMT5
Authors: Sun, L. / Wang, M. / Lv, Z. / Yang, N. / Liu, Y. / Bao, S. / Gong, W. / Xu, R.M.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 5
B: Protein arginine N-methyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,5883
Polymers169,4952
Non-polymers921
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-6 kcal/mol
Surface area54700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.560, 129.490, 149.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein arginine N-methyltransferase 5


Mass: 84747.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: prmt-5 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46580, EC: 2.1.1.125
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Tris, 9% PEG-5000MME, 5% Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→30.024 Å / Num. all: 39520 / Num. obs: 39417 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 43.05 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 20.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 3 / Num. unique all: 3868 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UA3

3ua3


Resolution: 3.005→30.024 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7542 / SU ML: 0.46 / σ(F): 1.34 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2885 1817 4.62 %RANDOM
Rwork0.2319 ---
all0.2346 39347 --
obs0.2346 39347 99.37 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.523 Å2 / ksol: 0.292 e/Å3
Displacement parametersBiso max: 297.9 Å2 / Biso mean: 99.3682 Å2 / Biso min: 2.69 Å2
Baniso -1Baniso -2Baniso -3
1--14.8337 Å2-0 Å2-0 Å2
2---10.5949 Å20 Å2
3----11.2793 Å2
Refinement stepCycle: LAST / Resolution: 3.005→30.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10192 0 6 147 10345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810756
X-RAY DIFFRACTIONf_angle_d0.85814197
X-RAY DIFFRACTIONf_chiral_restr0.061567
X-RAY DIFFRACTIONf_plane_restr0.0041803
X-RAY DIFFRACTIONf_dihedral_angle_d15.683850
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0051-3.11240.39911730.34473575374896
3.1124-3.23690.33841830.289537243907100
3.2369-3.3840.35251770.273937213898100
3.384-3.56220.30091820.242737393921100
3.5622-3.7850.29471800.229837333913100
3.785-4.07660.28561820.219337663948100
4.0766-4.48560.26281820.199737493931100
4.4856-5.13190.25671840.193338013985100
5.1319-6.4550.27261860.21638224008100
6.455-30.02540.24941880.21543900408898
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)
12.28780.3916-0.56826.9728-0.99090.3828-0.37320.43530.1176-2.29320.64610.5150.2241-0.107-0.29330.7806-0.3326-0.17570.22270.1464-0.023244.637939.494214.9524
23.3838-1.24690.28315.28-0.22680.3782-0.3604-0.3311-0.45090.06190.59042.5981-0.0357-0.1762-0.27660.00560.02460.10480.23040.46041.217.959815.30334.4384
32.4139-1.1991.04126.55710.1810.72080.07830.2969-0.3386-2.63190.25580.80270.08750.1746-0.3181.089-0.2217-0.28520.0979-0.03410.06642.6173-21.184115.8717
42.2748-0.4845-1.38554.04220.31221.2943-0.0664-0.31510.1539-1.50640.175-1.92160.17810.1369-0.07880.6559-0.06030.95780.096-0.15420.915575.28332.814917.7717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 41:330)
2X-RAY DIFFRACTION2(chain 'A' and (resseq 358:734))
3X-RAY DIFFRACTION3chain 'B' and (resseq 41:330)
4X-RAY DIFFRACTION4(chain 'B' and (resseq 358:734))

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