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- PDB-1iyg: Solution structure of RSGI RUH-001, a Fis1p-like and CGI-135 homo... -

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Basic information

Entry
Database: PDB / ID: 1iyg
TitleSolution structure of RSGI RUH-001, a Fis1p-like and CGI-135 homologous domain from a mouse cDNA
ComponentsHypothetical protein (2010003O14)
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MOUSE cDNA / FIS1P / CGI-135 / Hypothetical protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / Class I peroxisomal membrane protein import / : / : / : / positive regulation of mitochondrial calcium ion concentration / peroxisome fission / cellular response to peptide / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration ...: / Class I peroxisomal membrane protein import / : / : / : / positive regulation of mitochondrial calcium ion concentration / peroxisome fission / cellular response to peptide / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / autophagy of mitochondrion / protein targeting to mitochondrion / mitochondrial fission / regulation of mitochondrion organization / peroxisomal membrane / mitochondrial fusion / positive regulation of mitochondrial fission / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / positive regulation of protein targeting to membrane / positive regulation of intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / peroxisome / positive regulation of neuron apoptotic process / positive regulation of cytosolic calcium ion concentration / mitochondrial outer membrane / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein-containing complex / mitochondrion / identical protein binding
Similarity search - Function
Mitochondria fission 1 protein / Fis1, N-terminal tetratricopeptide repeat / Fis1, C-terminal tetratricopeptide repeat / Mitochondria fission protein Fis1, cytosolic domain / Fis1 N-terminal tetratricopeptide repeat / Fis1 C-terminal tetratricopeptide repeat / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial fission 1 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsOhashi, W. / Hirota, H. / Yamazaki, T. / Koshiba, S. / Hamada, T. / Yoshida, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of RSGI RUH-001, a Fis1p-like and CGI-135 homologous domain from a mouse cDNA
Authors: Ohashi, W. / Hirota, H. / Yamazaki, T. / Koshiba, S. / Hamada, T. / Yoshida, M. / Yokoyama, S.
History
DepositionAug 14, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 1.4Dec 27, 2023Group: 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: Hypothetical protein (2010003O14)


Theoretical massNumber of molelcules
Total (without water)15,1261
Polymers15,1261
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 / 100The submitted conformer models are those with the lowest number of target function
RepresentativeModel #1lowest target function

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Components

#1: Protein Hypothetical protein (2010003O14) / RSGI RUH-001


Mass: 15126.050 Da / Num. of mol.: 1 / Fragment: FIS1P-LIKE AND CGI-135 HOMOLOGOUS DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis system / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CQ92

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 0.6mM RSGI RUH-001 U-15N,13C; 20mM phosphate buffer NA, 100mM NaCl, 1mM DTT U-2H; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6brukercollection
NMRPipe2.1Delaglioprocessing
NMRView5.0.4Johnsondata analysis
CYANA1.0.6Guentertstructure solution
CYANA1.0.6Guentertrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: The submitted conformer models are those with the lowest number of target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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