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- PDB-3q7e: Crystal Structure of rat Protein Arginine Methyltransferase 1 (PR... -

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Basic information

Entry
Database: PDB / ID: 3q7e
TitleCrystal Structure of rat Protein Arginine Methyltransferase 1 (PRMT1)M48L mutant
ComponentsProtein arginine N-methyltransferase 1
KeywordsTRANSFERASE / Protein-Arginine N-Methyltransferases
Function / homology
Function and homology information


snoRNP binding / peptidyl-arginine omega-N-methylation / cellular response to methionine / GATOR1 complex binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Estrogen-dependent gene expression / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / positive regulation of hemoglobin biosynthetic process / Extra-nuclear estrogen signaling ...snoRNP binding / peptidyl-arginine omega-N-methylation / cellular response to methionine / GATOR1 complex binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Estrogen-dependent gene expression / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / positive regulation of hemoglobin biosynthetic process / Extra-nuclear estrogen signaling / protein-arginine omega-N monomethyltransferase activity / N-methyltransferase activity / histone H4R3 methyltransferase activity / regulation of BMP signaling pathway / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / protein methyltransferase activity / S-adenosylmethionine metabolic process / protein methylation / methylosome / protein-arginine N-methyltransferase activity / negative regulation of JNK cascade / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / methyl-CpG binding / cardiac muscle tissue development / positive regulation of p38MAPK cascade / mitogen-activated protein kinase p38 binding / histone methyltransferase activity / positive regulation of double-strand break repair via homologous recombination / negative regulation of megakaryocyte differentiation / positive regulation of TORC1 signaling / RNA splicing / positive regulation of erythrocyte differentiation / positive regulation of translation / liver regeneration / protein homooligomerization / neuron projection development / in utero embryonic development / lysosomal membrane / positive regulation of cell population proliferation / enzyme binding / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / 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 ...Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / 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 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsJohnson, S.J. / Porter, P.J. / Hevel, J.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Investigation of the molecular origins of protein-arginine methyltransferase I (PRMT1) product specificity reveals a role for two conserved methionine residues.
Authors: Gui, S. / Wooderchak, W.L. / Daly, M.P. / Porter, P.J. / Johnson, S.J. / Hevel, J.M.
History
DepositionJan 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7843
Polymers40,3751
Non-polymers4092
Water3,675204
1
A: Protein arginine N-methyltransferase 1
hetero molecules

A: Protein arginine N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5686
Polymers80,7502
Non-polymers8174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area3510 Å2
ΔGint-53 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.307, 87.307, 143.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: -x, y, -z.

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Components

#1: Protein Protein arginine N-methyltransferase 1


Mass: 40375.078 Da / Num. of mol.: 1 / Mutation: M48L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prmt1, Hrmt1l2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q63009, Transferases; Transferring one-carbon groups; Methyltransferases
#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.38 Å3/Da / Density % sol: 63.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Tris, 1.62 M ammonium phosphate monobasic, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 21, 2009
RadiationMonochromator: Ni Filter + Osmic Blue Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 27377 / Num. obs: 27377 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.78 % / Biso Wilson estimate: 35.7 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1923 / % possible all: 68

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.61 Å
Translation2.5 Å27.61 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHASER1.3.2phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OR8

1or8


Resolution: 2.2→27.692 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1377 5.03 %RANDOM
Rwork0.201 ---
all0.2033 27364 --
obs0.2033 27364 94.8 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.046 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 155.27 Å2 / Biso mean: 40.0357 Å2 / Biso min: 12.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.1661 Å2-0 Å20 Å2
2---0.1661 Å2-0 Å2
3---0.3321 Å2
Refinement stepCycle: LAST / Resolution: 2.2→27.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 27 204 2776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082633
X-RAY DIFFRACTIONf_angle_d1.1243565
X-RAY DIFFRACTIONf_chiral_restr0.074400
X-RAY DIFFRACTIONf_plane_restr0.004444
X-RAY DIFFRACTIONf_dihedral_angle_d13.458969
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 (%)
2.2002-2.27880.349710.30661851192268
2.2788-2.36990.34321250.29092211233683
2.3699-2.47770.32441370.27182643278099
2.4777-2.60830.32531500.27742669281999
2.6083-2.77160.34031440.230726872831100
2.7716-2.98530.28171370.232527302867100
2.9853-3.28530.22981470.196327192866100
3.2853-3.75970.26441610.184627412902100
3.7597-4.7330.18691580.150427892947100
4.733-27.69430.18891470.179729473094100
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)
11.61020.18950.21811.327-0.31680.35090.3034-0.7206-0.01340.0637-0.254-0.04170.15590.05490.03560.2514-0.05610.01240.43090.01370.2929.9635-1.7403-1.354
22.64552.12660.36571.56480.34481.26830.1059-0.1665-0.00440.0884-0.0540.02410.1138-0.3895-0.06690.1392-0.0617-0.00960.24690.01130.183916.526-10.5823-6.9516
31.71321.3305-1.28531.3508-1.38261.2722-0.0982-0.0444-0.2347-0.19530.0017-0.12250.115-0.10970.07420.1878-0.07150.01920.1812-0.04880.189828.5907-10.3845-17.9439
42.3246-1.08773.25443.38260.44499.0808-0.25270.1359-0.5670.10020.63320.0993-0.45270.8676-0.38670.21470.0060.05850.25210.00780.209656.06887.2523-12.1325
50.38190.48530.90641.07480.61992.48490.11950.2813-0.3838-0.2074-0.0645-0.13720.09690.5596-0.06520.21320.08120.03720.36880.02780.341963.5588-1.8954-7.5076
60.9212-0.0472-0.31840.16950.3090.56640.0078-0.1031-0.05820.0020.03660.0247-0.15760.04250.01770.2298-0.0550.00560.225-0.01730.233342.88085.0672-20.2497
71.01180.0105-0.16520.3504-0.42050.444-0.03560.15060.1222-0.1544-0.04530.07660.0436-0.0570.08890.2083-0.07560.02190.1729-0.04440.1241.5094-2.359-26.5194
81.54850.0109-0.34170.1206-0.39960.84750.27110.01090.2746-0.0861-0.04660.0522-0.1025-0.1607-0.17730.1846-0.04810.00430.22230.0260.199232.18362.4868-17.6592
92.30931.6293-0.51452.7123-0.06210.9309-0.02450.0898-0.3632-0.1041-0.084-0.45760.0120.12160.04830.1169-0.0226-0.00540.11440.01340.123850.4704-3.2227-22.943
101.65340.23840.16790.26810.16350.446-0.03530.0935-0.5033-0.184-0.1205-0.4060.0830.18070.09130.2145-0.06820.01520.29070.01810.277453.9614-3.1544-24.9202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 40:53)A40 - 53
2X-RAY DIFFRACTION2(chain A and resid 54:140)A54 - 140
3X-RAY DIFFRACTION3(chain A and resid 141:184)A141 - 184
4X-RAY DIFFRACTION4(chain A and resid 185:196)A185 - 196
5X-RAY DIFFRACTION5(chain A and resid 197:216)A197 - 216
6X-RAY DIFFRACTION6(chain A and resid 217:236)A217 - 236
7X-RAY DIFFRACTION7(chain A and resid 237:265)A237 - 265
8X-RAY DIFFRACTION8(chain A and resid 266:299)A266 - 299
9X-RAY DIFFRACTION9(chain A and resid 300:328)A300 - 328
10X-RAY DIFFRACTION10(chain A and resid 329:353)A329 - 353

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