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- PDB-1j3t: Solution structure of the second SH3 domain of human intersectin ... -

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Basic information

Entry
Database: PDB / ID: 1j3t
TitleSolution structure of the second SH3 domain of human 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 / presynaptic membrane / Clathrin-mediated endocytosis / cell differentiation ...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 / presynaptic membrane / Clathrin-mediated endocytosis / cell differentiation / molecular adaptor activity / 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 / EH 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. / C2 domain / Protein kinase C conserved region 2 (CalB) / 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 / Src homology 3 domains / SH3 type barrels. / 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, restrained molecular dynamics
AuthorsNameki, N. / Koshiba, S. / Tochio, N. / Kobayashi, N. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the second SH3 domain of human intersectin 2 (KIAA1256)
Authors: Nameki, N. / Koshiba, S. / Tochio, N. / Kobayashi, N. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionFeb 13, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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)8,0711
Polymers8,0711
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 #1fewest violations, lowest energy

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Components

#1: Protein Intersectin 2 /


Mass: 8070.892 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: Kazusa cDNA hh15293 / Plasmid: P021015-57 / References: UniProt: Q9NZM3

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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: 1.5mM SH3 domain U-15N, 13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM Na / 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: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.771Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
OPALpGuentert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations, 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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