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- PDB-3ua3: Crystal Structure of Protein Arginine Methyltransferase PRMT5 in ... -

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Basic information

Entry
Database: PDB / ID: 3ua3
TitleCrystal Structure of Protein Arginine Methyltransferase PRMT5 in complex with SAH
ComponentsProtein arginine N-methyltransferase 5
KeywordsTRANSFERASE / TIM-barrel / Rossmann Fold / beta-barrel / symmetric arginine dimethylase / SAM binding / 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 H3K37 methyltransferase activity / histone H4R3 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / protein-arginine N-methyltransferase activity / histone H2AQ104 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
S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 5
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 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 20, 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 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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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)171,8594
Polymers171,0902
Non-polymers7692
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-6 kcal/mol
Surface area53710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.376, 129.381, 149.315
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: 85544.961 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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.83 Å3/Da / Density % sol: 56.59 %
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: Apr 27, 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 Å / Num. obs: 39581 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 38.68 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 27.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3856 / % possible all: 100

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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: SAD / Resolution: 3→29.952 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7808 / SU ML: 0.41 / σ(F): 1.34 / Phase error: 28.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2808 1828 4.62 %RANDOM
Rwork0.223 ---
all0.2257 39556 --
obs0.2257 39556 99.94 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.071 Å2 / ksol: 0.276 e/Å3
Displacement parametersBiso max: 313.22 Å2 / Biso mean: 84.3059 Å2 / Biso min: 2.31 Å2
Baniso -1Baniso -2Baniso -3
1--14.5124 Å2-0 Å2-0 Å2
2---11.3244 Å20 Å2
3----10.0372 Å2
Refinement stepCycle: LAST / Resolution: 3→29.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10539 0 52 146 10737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911179
X-RAY DIFFRACTIONf_angle_d0.94214761
X-RAY DIFFRACTIONf_chiral_restr0.0651634
X-RAY DIFFRACTIONf_plane_restr0.0041874
X-RAY DIFFRACTIONf_dihedral_angle_d22.636619
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 (%)
3-3.10710.36981800.310337013881100
3.1071-3.23140.32361810.267237363917100
3.2314-3.37830.33671800.250137223902100
3.3783-3.55610.29771800.231437273907100
3.5561-3.77850.27611810.213237323913100
3.7785-4.06960.26291830.204737623945100
4.0696-4.47790.23561820.180737613943100
4.4779-5.12310.24741830.179938023985100
5.1231-6.4440.26831860.225438244010100
6.444-29.95370.27681920.23183961415399
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)
12.48831.61050.17225.9364-1.18070.4214-0.6640.39360.3124-2.12740.76120.66280.30.0091-0.08780.7128-0.3031-0.23780.20390.1671-0.025344.757639.67114.7442
21.9646-1.36870.68673.2731-0.14930.4626-0.3445-0.3408-0.3730.03590.52531.9672-0.0461-0.1851-0.20320.03560.02640.06920.29750.41821.145818.42515.836633.6317
31.8506-0.6140.89463.75640.19910.4998-0.02390.2783-0.2372-2.00740.18250.51980.14910.1083-0.15641.0058-0.1749-0.19180.07580.00470.067242.7009-20.995515.6334
41.2223-1.0071-0.91682.8643-0.12081.0727-0.1067-0.19880.1047-1.3642-0.0602-1.66420.3390.06060.18140.6656-0.00660.9370.0871-0.06140.844774.69182.663217.5963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 45:330)
2X-RAY DIFFRACTION2(chain 'A' and (resseq 358:734)) or (chain 'A' and (resseq 743))
3X-RAY DIFFRACTION3chain 'B' and (resseq 43:330)
4X-RAY DIFFRACTION4(chain 'B' and (resseq 358:734)) or (chain 'B' and (resseq 743))

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