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- PDB-1uhc: Solution Structure of RSGI RUH-002, a SH3 Domain of KIAA1010 prot... -

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Basic information

Entry
Database: PDB / ID: 1uhc
TitleSolution Structure of RSGI RUH-002, a SH3 Domain of KIAA1010 protein [Homo sapiens]
ComponentsKIAA1010 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta barrel / SH3 / human cDNA / 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 ...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 / 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
Dynamin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsAbe, T. / Hirota, H. / Kobayashi, N. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of RSGI RUH-002, a SH3 Domain of KIAA1010 protein [Homo sapiens]
Authors: Abe, T. / Hirota, H. / Kobayashi, N. / Hayashi, F. / Yokoyama, S.
History
DepositionJun 28, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 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_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 1.4Dec 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)8,5731
Polymers8,5731
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 #1the structure with the lowest energy and score of target function was selected.

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Components

#1: Protein KIAA1010 protein


Mass: 8573.360 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 system / Gene: Kazusa cDNA hj05262 / Plasmid: P021015-01 / 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: 1mM RSGI RUH-002 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 NaCl / 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.816Kobayashi, N.data analysis
CYANA1.0.7Guentert, Prefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: the structure with the lowest energy and score of target function was selected.
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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