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- PDB-1udl: The solution structure of the fifth SH3 domain of intersectin 2 (... -

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Basic information

Entry
Database: PDB / ID: 1udl
TitleThe solution structure of the fifth SH3 domain of intersectin 2 (KIAA1256)
Componentsintersectin 2
KeywordsENDOCYTOSIS/EXOCYTOSIS / BETA BARREL / SH3 DOMAIN / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


clathrin-dependent synaptic vesicle endocytosis / positive regulation of dendrite extension / endosomal transport / intracellular vesicle / RHOU GTPase cycle / guanyl-nucleotide exchange factor activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / presynaptic membrane / molecular adaptor activity ...clathrin-dependent synaptic vesicle endocytosis / positive regulation of dendrite extension / endosomal transport / intracellular vesicle / RHOU GTPase cycle / guanyl-nucleotide exchange factor activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / presynaptic membrane / molecular adaptor activity / cell differentiation / centrosome / calcium ion binding / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Intersectin-2, first SH3 domain / Intersectin-2, second SH3 domain / Intersectin-2, third SH3 domain / Intersectin-2, fourth SH3 domain / Intersectin-2, fifth SH3 domain / Pleckstrin homology domain / : / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain ...Intersectin-2, first SH3 domain / Intersectin-2, second SH3 domain / Intersectin-2, third SH3 domain / Intersectin-2, fourth SH3 domain / Intersectin-2, fifth SH3 domain / Pleckstrin homology domain / : / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Variant SH3 domain / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / SH3 Domains / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / EF-hand, calcium binding motif / SH3 type barrels. / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGoroncy, A. / Kigawa, T. / Koshiba, S. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: The solution structure of the fifth SH3 domain of intersectin 2 (KIAA1256)
Authors: Goroncy, A. / Kigawa, T. / Koshiba, S. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S.
History
DepositionMay 1, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2003Provider: 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_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 1.4Dec 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: intersectin 2


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 / 100target function
RepresentativeModel #1lowest target function

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Components

#1: Protein intersectin 2 / KIAA1256


Mass: 10492.481 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 synthesis system / Gene: KAZUSA cDNA hh15293 / Plasmid: P021015-68 / References: UniProt: Q9NZM3

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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: 1.29mM SH3 domain, 20mM phosphate buffer, 100mM NaCl, 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6 / 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: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5.0.4BRUCE A. JOHNSONdata analysis
NMRPipe20020425FRANK DELAGLIOprocessing
CYANA2.0.17P.Guntertrefinement
XwinNMR2.6BRUKERcollection
KUJIRA0.801NAOHIRO KOBAYASHIdata analysis
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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