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- PDB-1ori: Structure of the predominant protein arginine methyltransferase PRMT1 -

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Basic information

Entry
Database: PDB / ID: 1ori
TitleStructure of the predominant protein arginine methyltransferase PRMT1
ComponentsProtein arginine N-methyltransferase 1
KeywordsTRANSFERASE / protein arginine methylation AdoMet-dependent methylation
Function / homology
Function and homology information


snoRNP binding / peptidyl-arginine omega-N-methylation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / Estrogen-dependent gene expression / RMTs methylate histone arginines / GATOR1 complex binding / Extra-nuclear estrogen signaling / positive regulation of hemoglobin biosynthetic process / protein-arginine omega-N monomethyltransferase activity ...snoRNP binding / peptidyl-arginine omega-N-methylation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / Estrogen-dependent gene expression / RMTs methylate histone arginines / GATOR1 complex binding / Extra-nuclear estrogen signaling / positive regulation of hemoglobin biosynthetic process / protein-arginine omega-N monomethyltransferase activity / N-methyltransferase activity / regulation of BMP signaling pathway / protein-arginine omega-N asymmetric methyltransferase activity / S-adenosylmethionine metabolic process / regulation of megakaryocyte differentiation / type I protein arginine methyltransferase / histone H4R3 methyltransferase activity / protein methyltransferase activity / protein methylation / S-adenosylmethionine-dependent methyltransferase activity / protein-arginine N-methyltransferase activity / cellular response to methionine / methylosome / S-adenosyl-L-methionine binding / methyl-CpG binding / positive regulation of p38MAPK cascade / cardiac muscle tissue development / negative regulation of JNK cascade / histone methyltransferase activity / mitogen-activated protein kinase p38 binding / negative regulation of megakaryocyte differentiation / positive regulation of double-strand break repair via homologous recombination / positive regulation of TORC1 signaling / liver regeneration / RNA splicing / positive regulation of erythrocyte differentiation / positive regulation of translation / protein homooligomerization / neuron projection development / in utero embryonic development / chromatin remodeling / lysosomal membrane / positive regulation of cell population proliferation / DNA damage response / regulation of DNA-templated transcription / enzyme binding / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 / Unknown ligand / Protein arginine N-methyltransferase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, X. / Cheng, X.
CitationJournal: Structure / Year: 2003
Title: Structure of the Predominant Protein Arginine Methyltransferase PRMT1 and Analysis of its Binding to Substrate Peptides
Authors: Zhang, X. / Cheng, X.
History
DepositionMar 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0124
Polymers39,6271
Non-polymers3843
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Protein arginine N-methyltransferase 1
hetero molecules

A: Protein arginine N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0238
Polymers79,2552
Non-polymers7696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Buried area4380 Å2
ΔGint-33 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.27, 88.27, 145.14
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-420-

HOH

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Components

#1: Protein Protein arginine N-methyltransferase 1


Mass: 39627.297 Da / Num. of mol.: 1 / Fragment: M11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: HRMT1L2 OR PRMT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63009, 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: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 3.57 Å3/Da / Density % sol: 65.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: ammonium phosphate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
2100 mMTris1reservoirpH9.0
31.6 Mammonium phosphate monobasic1reservoirpH4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 20200 / Num. obs: 20200 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.07 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.2
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 6.7 / Num. unique all: 952 / % possible all: 96.2
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 102483 / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F3L

1f3l


Resolution: 2.5→24.18 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1506 -RANDOM
Rwork0.199 ---
all-19123 --
obs-19123 93.2 %-
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2---0.85 Å20 Å2
3---1.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-24.18 Å
Luzzati sigma a0.38 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 33 129 2694
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d1.3
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_improper_angle_d0.68
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.028
RfactorNum. reflection% reflection
Rfree0.365 175 -
Rwork0.299 --
obs-1855 81.2 %
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.68

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