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- PDB-2ega: Solution structure of the first SH3 domain from human KIAA0418 protein -

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Basic information

Entry
Database: PDB / ID: 2ega
TitleSolution structure of the first SH3 domain from human KIAA0418 protein
ComponentsSH3 and PX domain-containing protein 2A
KeywordsSIGNALING PROTEIN / SH3 domain / KIAA0418 protein / SH3MD1 / SH3 multiple domains 1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Invadopodia formation / osteoclast fusion / superoxide-generating NADPH oxidase activator activity / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3-phosphate binding / superoxide anion generation / phosphatidylinositol-4-phosphate binding / anchoring junction / podosome ...Invadopodia formation / osteoclast fusion / superoxide-generating NADPH oxidase activator activity / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3-phosphate binding / superoxide anion generation / phosphatidylinositol-4-phosphate binding / anchoring junction / podosome / superoxide metabolic process / CDC42 GTPase cycle / phosphatidylinositol-4,5-bisphosphate binding / cell projection / protease binding / in utero embryonic development / cytosol / cytoplasm
Similarity search - Function
SH3PXD2A, SH3 domain 3 / SH3PXD2A, SH3 domain 1 / SH3PXD2A, SH3 domain 2 / SH3PXD2A, SH3 domain 4 / SH3PXD2A, SH3 domain 5 / SH3PXD2, PX domain / : / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain ...SH3PXD2A, SH3 domain 3 / SH3PXD2A, SH3 domain 1 / SH3PXD2A, SH3 domain 2 / SH3PXD2A, SH3 domain 4 / SH3PXD2A, SH3 domain 5 / SH3PXD2, PX domain / : / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Variant SH3 domain / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
SH3 and PX domain-containing protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsInoue, K. / Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Solution structure of the first SH3 domain from human KIAA0418 protein
Authors: Inoue, K. / Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S.
History
DepositionFeb 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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 1.3May 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: SH3 and PX domain-containing protein 2A


Theoretical massNumber of molelcules
Total (without water)7,5321
Polymers7,5321
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, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein SH3 and PX domain-containing protein 2A / KIAA0418 protein / SH3 multiple domains protein 1 / Five SH3 domain-containing protein / Adaptor protein TKS5


Mass: 7531.977 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: SH3MD1 / Plasmid: P050905-04 / References: UniProt: Q5TCZ1

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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: 1.13mM U-15N, 13C-labeled protein; 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: 298 K

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NMR measurement

NMR spectrometerType: JEOL ECA / Manufacturer: JEOL / Model: ECA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Delta NMR4.3.2JEOLcollection
NMRPipe20060324Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9807Kobayashi, N.data analysis
CYANA2.1Guntert, P.structure solution
CYANA2.1Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
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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