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- PDB-1spk: Solution Structure of RSGI RUH-010, an SH3 Domain from Mouse cDNA -

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Basic information

Entry
Database: PDB / ID: 1spk
TitleSolution Structure of RSGI RUH-010, an SH3 Domain from Mouse cDNA
ComponentsRIKEN cDNA 1300006M19
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SH3 domain / five-stranded barrel / mouse cDNA / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / regulation of insulin receptor signaling pathway / plasma membrane organization / actin crosslink formation / proline-rich region binding / positive regulation of actin filament polymerization / actin filament bundle assembly / response to bacterium / actin cytoskeleton / actin binding ...: / regulation of insulin receptor signaling pathway / plasma membrane organization / actin crosslink formation / proline-rich region binding / positive regulation of actin filament polymerization / actin filament bundle assembly / response to bacterium / actin cytoskeleton / actin binding / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
I-BAR domain containing protein IRTKS / IRTKS, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / Src homology 3 domains ...I-BAR domain containing protein IRTKS / IRTKS, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsSuzuki, Y. / Abe, T. / Hirota, H. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of RSGI RUH-010, an SH3 Domain from Mouse cDNA
Authors: Suzuki, Y. / Abe, T. / Hirota, H. / Hayashi, F. / Yokoyama, S.
History
DepositionMar 17, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIKEN cDNA 1300006M19


Theoretical massNumber of molelcules
Total (without water)7,6641
Polymers7,6641
Non-polymers00
Water0
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, structures with the lowest energy, target function
RepresentativeModel #1lowest energy, target function

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Components

#1: Protein RIKEN cDNA 1300006M19 / RSGI RUH-010


Mass: 7664.490 Da / Num. of mol.: 1
Fragment: Putative SH3 domain(Residues 343-401 in seq. db No.)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 1300006M19 / Organ: liver / Plasmid: P030120-88 / References: UniProt: Q9DBJ3

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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
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.0mM protein; 20mM sodium phosphate; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.853Kobayashi, N.data analysis
CYANA1.0.7Guntert, P.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy, target function
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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