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- PDB-2djq: The solution structure of the first SH3 domain of mouse SH3 domai... -

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Basic information

Entry
Database: PDB / ID: 2djq
TitleThe solution structure of the first SH3 domain of mouse SH3 domain containing ring finger 2
ComponentsSH3 domain containing ring finger 2
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SH3 domain / Mus musculus 0 day neonate head cDNA / RIKEN full-length enriched library / clone:4831401O22 / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of phosphatase activity / protein phosphatase 1 binding / negative regulation of JNK cascade / protein phosphatase inhibitor activity / phosphatase binding / protein autoubiquitination / negative regulation of protein ubiquitination / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity ...negative regulation of phosphatase activity / protein phosphatase 1 binding / negative regulation of JNK cascade / protein phosphatase inhibitor activity / phosphatase binding / protein autoubiquitination / negative regulation of protein ubiquitination / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein ubiquitination / positive regulation of cell migration / negative regulation of apoptotic process / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
E3 ubiquitin-protein ligase SH3RF2 / E3 ubiquitin-protein ligase SH3RF2, first SH3 domain / E3 ubiquitin-protein ligase SH3RF2, second SH3 domain / SH3RF2, third SH3 domain / Ring finger domain / Variant SH3 domain / Variant SH3 domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SH3 Domains ...E3 ubiquitin-protein ligase SH3RF2 / E3 ubiquitin-protein ligase SH3RF2, first SH3 domain / E3 ubiquitin-protein ligase SH3RF2, second SH3 domain / SH3RF2, third SH3 domain / Ring finger domain / Variant SH3 domain / Variant SH3 domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SH3 Domains / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / SH3 domain / Zinc finger RING-type profile. / Zinc finger, RING-type / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase SH3RF2 / E3 ubiquitin-protein ligase SH3RF2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSasagawa, A. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: The solution structure of the first SH3 domain of mouse SH3 domain containing ring finger 2
Authors: Sasagawa, A. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 5, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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: SH3 domain containing ring finger 2


Theoretical massNumber of molelcules
Total (without water)7,1481
Polymers7,1481
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 least restraint violations
RepresentativeModel #1lowest energy,fewest violations

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Components

#1: Protein SH3 domain containing ring finger 2


Mass: 7147.915 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Gene: Sh3rf2 / Plasmid: P050425-13 / Production host: Cell free synthesis / References: UniProt: Q8C122, UniProt: Q8BZT2*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
1223D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.31mM SH3 domain U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: mbient / 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
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, Fprocessing
NMNMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.933Kobayashi, 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,fewest violations
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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