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- PDB-1v85: Sterile alpha motif (SAM) domain of mouse bifunctional apoptosis ... -

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Basic information

Entry
Database: PDB / ID: 1v85
TitleSterile alpha motif (SAM) domain of mouse bifunctional apoptosis regulator
Componentssimilar to ring finger protein 36
KeywordsAPOPTOSIS / neuron / cell death / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of IRE1-mediated unfolded protein response / caspase binding / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / protein polyubiquitination / ubiquitin protein ligase activity / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process ...negative regulation of IRE1-mediated unfolded protein response / caspase binding / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / protein polyubiquitination / ubiquitin protein ligase activity / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / membrane => GO:0016020 / apoptotic process / endoplasmic reticulum membrane / negative regulation of apoptotic process / endoplasmic reticulum / membrane / metal ion binding
Similarity search - Function
Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Sterile alpha motif/pointed domain superfamily / Ring finger / Zinc finger RING-type profile. ...Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Sterile alpha motif/pointed domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / DNA polymerase; domain 1 / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bifunctional apoptosis regulator / Bifunctional apoptosis regulator
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGoroncy, A. / Kigawa, T. / Koshiba, S. / Hayashi, F. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Sterile alpha motif (SAM) domain of mouse bifunctional apoptosis regulator
Authors: Goroncy, A. / Kigawa, T. / Koshiba, S. / Hayashi, F. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S.
History
DepositionDec 29, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_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 / _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: similar to ring finger protein 36


Theoretical massNumber of molelcules
Total (without water)10,2951
Polymers10,2951
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
RepresentativeModel #1lowest target function

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Components

#1: Protein similar to ring finger protein 36 / bifunctional apoptosis regulator


Mass: 10295.476 Da / Num. of mol.: 1 / Fragment: sterile alpha motif (SAM) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: RIKEN CDNA 3010001A07 / Plasmid: P030120-59 / References: UniProt: Q9CXY3, UniProt: Q8R079*PLUS

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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: 1.14mM SAM domain, 20mM phosphate buffer Na, 100mM NaCl, 1mM d-DTT, 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVARIANcollection
NMRPipe20020425FRANK DELAGLIOprocessing
NMRView5.0.14BRUCE A. JOHNSONdata analysis
KUJIRA0.863NAOHIRO KOBAYASHIdata analysis
CYANA2.0.17PETER GUENTERTrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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