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- PDB-2yu0: Solution structures of the PAAD_DAPIN domain of mus musculus inte... -

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Basic information

Entry
Database: PDB / ID: 2yu0
TitleSolution structures of the PAAD_DAPIN domain of mus musculus interferon-activatable protein 205
ComponentsInterferon-activable protein 205
KeywordsSIGNALING PROTEIN / PAAD_DAPIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cellular response to interferon-alpha / nuclear inclusion body / transcription factor binding / inner ear development / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of osteoblast differentiation / cellular response to interferon-beta / Neutrophil degranulation / activation of innate immune response / nuclear periphery ...cellular response to interferon-alpha / nuclear inclusion body / transcription factor binding / inner ear development / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of osteoblast differentiation / cellular response to interferon-beta / Neutrophil degranulation / activation of innate immune response / nuclear periphery / positive regulation of interleukin-1 beta production / transcription coregulator activity / response to bacterium / DNA-binding transcription repressor activity, RNA polymerase II-specific / double-stranded DNA binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleolus / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / PAAD/DAPIN/Pyrin domain / Death Domain, Fas ...HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / Death-like domain superfamily / Nucleic acid-binding, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Interferon-activable protein 211 / Interferon-activable protein 204
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSato, M. / Tochio, N. / Koshiba, S. / Watanabe, M. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structures of the PAAD_DAPIN domain of mus musculus interferon-activatable protein 205
Authors: Sato, M. / Tochio, N. / Koshiba, S. / Watanabe, M. / Harada, T. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 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: Interferon-activable protein 205


Theoretical massNumber of molelcules
Total (without water)10,4921
Polymers10,4921
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 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Interferon-activable protein 205 / IFI-205 / D3 protein


Mass: 10491.929 Da / Num. of mol.: 1 / Fragment: PAAD_DAPIN, UNP residues 8-88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Gene: Ifi205 / Plasmid: P051212-10 / References: UniProt: Q08619, UniProt: P0DOV1*PLUS

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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

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Sample preparation

DetailsContents: 0.5mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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