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- PDB-1x2p: Solution structure of the SH3 domain of the Protein arginine N-me... -

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Basic information

Entry
Database: PDB / ID: 1x2p
TitleSolution structure of the SH3 domain of the Protein arginine N-methyltransferase 2
ComponentsProtein arginine N-methyltransferase 2
KeywordsTRANSFERASE / SH3 domain / Protein arginine N-methyltransferase / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


nuclear progesterone receptor binding / histone H3R8 methyltransferase activity / developmental cell growth / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methylation / protein-arginine N-methyltransferase activity / nuclear retinoic acid receptor binding / regulation of androgen receptor signaling pathway / peroxisome proliferator activated receptor binding ...nuclear progesterone receptor binding / histone H3R8 methyltransferase activity / developmental cell growth / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methylation / protein-arginine N-methyltransferase activity / nuclear retinoic acid receptor binding / regulation of androgen receptor signaling pathway / peroxisome proliferator activated receptor binding / histone H3 methyltransferase activity / nuclear thyroid hormone receptor binding / negative regulation of NF-kappaB transcription factor activity / nuclear androgen receptor binding / negative regulation of G1/S transition of mitotic cell cycle / histone methyltransferase activity / nuclear estrogen receptor binding / transcription coactivator activity / chromatin remodeling / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / signal transduction / protein homodimerization activity / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Methyltransferase small domain / Methyltransferase small domain / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Protein arginine N-methyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsChikayama, E. / Kigawa, T. / Saito, K. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the SH3 domain of the Protein arginine N-methyltransferase 2
Authors: Chikayama, E. / Kigawa, T. / Saito, K. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionApr 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 2


Theoretical massNumber of molelcules
Total (without water)7,2381
Polymers7,2381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function,structures with the lowest energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein arginine N-methyltransferase 2


Mass: 7237.906 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: HRMT1L1 / Plasmid: P040531-04
References: UniProt: P55345, Transferases; Transferring one-carbon groups; Methyltransferases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.08mM SH3 domain U-15N,13C; 20mM d-tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5Johnson, B.A.data analysis
KUJIRA0.9Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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