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- PDB-1ug1: SH3 domain of Hypothetical protein BAA76854.1 -

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Basic information

Entry
Database: PDB / ID: 1ug1
TitleSH3 domain of Hypothetical protein BAA76854.1
ComponentsKIAA1010 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SH3 domain / Hypothetical protein BAA76854.1 / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Golgi stack / regulation of small GTPase mediated signal transduction / CDC42 GTPase cycle / cilium assembly / guanyl-nucleotide exchange factor activity / cell-cell junction / presynapse / regulation of cell shape / cytoskeleton / intracellular signal transduction ...Golgi stack / regulation of small GTPase mediated signal transduction / CDC42 GTPase cycle / cilium assembly / guanyl-nucleotide exchange factor activity / cell-cell junction / presynapse / regulation of cell shape / cytoskeleton / intracellular signal transduction / synapse / Golgi apparatus / cytosol / cytoplasm
Similarity search - Function
Dynamin-binding protein, first N-terminal SH3 domain / Dynamin-binding protein, second N-terminal SH3 domain / Dynamin-binding protein, third N-terminal SH3 domain / Dynamin-binding protein, first C-terminal SH3 domain / BAR domain / BAR domain profile. / BAR / BAR domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. ...Dynamin-binding protein, first N-terminal SH3 domain / Dynamin-binding protein, second N-terminal SH3 domain / Dynamin-binding protein, third N-terminal SH3 domain / Dynamin-binding protein, first C-terminal SH3 domain / BAR domain / BAR domain profile. / BAR / BAR domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / AH/BAR domain superfamily / 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. / SH3 Domains / SH3 domain / 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
Dynamin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsNagata, T. / Muto, Y. / Kamewari, Y. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. ...Nagata, T. / Muto, Y. / Kamewari, Y. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Kobayashi, N. / Tanaka, A. / Osanai, T. / Matsuo, Y. / Ohara, O. / Nagase, T. / Kikuno, R. / Nakayama, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: NMR structure of SH3 domain of Hypothetical protein BAA76854.1
Authors: Nagata, T. / Muto, Y. / Kamewari, Y. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Kobayashi, N. / ...Authors: Nagata, T. / Muto, Y. / Kamewari, Y. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Kobayashi, N. / Tanaka, A. / Osanai, T. / Matsuo, Y. / Ohara, O. / Nagase, T. / Kikuno, R. / Nakayama, M. / Yokoyama, S.
History
DepositionJun 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 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: KIAA1010 protein


Theoretical massNumber of molelcules
Total (without water)9,8731
Polymers9,8731
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein KIAA1010 protein / Hypothetical protein BAA76854.1


Mass: 9872.934 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 hj05262 / Plasmid: P021015-49 / References: UniProt: Q6XZF7

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

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Sample preparation

DetailsContents: 1.0mM PROTEIN U-15N, 13C; 20mM Phosphate buffer Na; 100mM NaCl; 0.02% NaN3; 90% H2O, 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: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5.0.4Johnsondata analysis
CYANA1Guentertstructure solution
NMRPipe1.8Delaglioprocessing
KUJIRA0.816Kobayashi, N.data analysis
CYANA1Guentertrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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