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- PDB-1or8: Structure of the Predominant protein arginine methyltransferase PRMT1 -

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Basic information

Entry
Database: PDB / ID: 1or8
TitleStructure of the Predominant protein arginine methyltransferase PRMT1
Components
  • Protein arginine N-methyltransferase 1
  • Substrate peptide
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 / 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 ...snoRNP binding / peptidyl-arginine omega-N-methylation / 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 / methylosome / protein methylation / protein-arginine N-methyltransferase activity / S-adenosyl-L-methionine binding / negative regulation of JNK cascade / cardiac muscle tissue development / methyl-CpG binding / positive regulation of p38MAPK cascade / mitogen-activated protein kinase p38 binding / histone methyltransferase activity / negative regulation of megakaryocyte differentiation / S-adenosylmethionine-dependent methyltransferase activity / RNA splicing / positive regulation of erythrocyte differentiation / liver regeneration / positive regulation of translation / protein homooligomerization / neuron projection development / in utero embryonic development / positive regulation of cell population proliferation / enzyme binding / protein-containing complex / nucleoplasm / nucleus / identical protein binding / cytosol / cytoplasm
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 / Unknown ligand / Protein arginine N-methyltransferase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 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
Remark 400THE ENTRY PRESENTS A STRUCTURE OF A COMPLEX BETWEEN PROTEIN ARGININE N-METHYLTRANSFERASE 1 AND ...THE ENTRY PRESENTS A STRUCTURE OF A COMPLEX BETWEEN PROTEIN ARGININE N-METHYLTRANSFERASE 1 AND SUBSTRATE PEPTIDE (19 RESIDUES). THE COORDINATES PRESENTED IN THE FILE FOR PEPTIDE SUBSTRATE ARE FOR FOUR POSSIBLE ALTERNATE LOCATION AS CHAINS B, C, D AND E. REMARKS 465, 470 AND SHORT CONTACTS SHOULD BE VIEWED IN THIS CONTEXT.

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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
B: Substrate peptide
C: Substrate peptide
D: Substrate peptide
E: Substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5289
Polymers45,9595
Non-polymers5694
Water3,063170
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)79,67310
Polymers78,5362
Non-polymers1,1378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Buried area4750 Å2
ΔGint-22 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.5, 86.5, 142.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number91
Space group name H-MP4122

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Components

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Protein / Protein/peptide , 2 types, 5 molecules ABCDE

#1: Protein Protein arginine N-methyltransferase 1


Mass: 39267.855 Da / Num. of mol.: 1 / Fragment: S14
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: Protein/peptide
Substrate peptide / Coordinate model: Cα atoms only (Chain-E)


Mass: 1672.792 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: chemically synthesized

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Non-polymers , 4 types, 174 molecules

#3: 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
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.7
Details: ammonium phosphate, pH 4.7, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: May 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. all: 22428 / Num. obs: 22428 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.455 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 20.7
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.2 / Num. unique all: 691 / % possible all: 61.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F3L
Resolution: 2.35→24.65 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1619 -RANDOM
Rwork0.195 ---
all-21747 --
obs-21747 96.3 %-
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-24.65 Å
Luzzati sigma a0.3 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.35→24.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2577 0 43 170 2790
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d1.4
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_improper_angle_d0.62
LS refinement shellResolution: 2.35→2.46 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.32 115 -
Rwork0.256 --
obs-1427 54.6 %

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