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- PDB-1uen: Solution Structure of The Third Fibronectin III Domain of Human K... -

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Basic information

Entry
Database: PDB / ID: 1uen
TitleSolution Structure of The Third Fibronectin III Domain of Human KIAA0343 Protein
ComponentsKIAA0343 protein
KeywordsCELL ADHESION / Immunoglobulin-like Beta-Sandwich Fold / Fibronectin Type III / NG-CAM Related Cell Adhesion Molecule / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


clustering of voltage-gated sodium channels / protein binding involved in heterotypic cell-cell adhesion / cell-cell adhesion mediator activity / NrCAM interactions / Neurofascin interactions / axon initial segment / axonal fasciculation / neuronal action potential propagation / Interaction between L1 and Ankyrins / ankyrin binding ...clustering of voltage-gated sodium channels / protein binding involved in heterotypic cell-cell adhesion / cell-cell adhesion mediator activity / NrCAM interactions / Neurofascin interactions / axon initial segment / axonal fasciculation / neuronal action potential propagation / Interaction between L1 and Ankyrins / ankyrin binding / regulation of axon extension / regulation of postsynapse organization / retinal ganglion cell axon guidance / regulation of neuron projection development / synapse assembly / positive regulation of neuron differentiation / axonogenesis / axon guidance / central nervous system development / neuron migration / postsynaptic density membrane / brain development / cell-cell adhesion / protein localization / angiogenesis / neuron projection / axon / external side of plasma membrane / glutamatergic synapse / extracellular region / plasma membrane
Similarity search - Function
Neurofascin/L1/NrCAM, C-terminal domain / Bravo-like intracellular region / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. ...Neurofascin/L1/NrCAM, C-terminal domain / Bravo-like intracellular region / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neuronal cell adhesion molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsMiyamoto, K. / Kigawa, T. / Hayashi, F. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of The Third Fibronectin III Domain of Human KIAA0343 Protein
Authors: Miyamoto, K. / Kigawa, T. / Hayashi, F. / Inoue, M. / Yokoyama, S.
History
DepositionMay 19, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 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: KIAA0343 protein


Theoretical massNumber of molelcules
Total (without water)13,5861
Polymers13,5861
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, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein KIAA0343 protein


Mass: 13586.198 Da / Num. of mol.: 1 / Fragment: Fibronectin Type III Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KAZUSA cDNA hg01457 / Plasmid: P021007-38 / References: UniProt: Q92823

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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
131

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Sample preparation

DetailsContents: 1.2mM fibronectin type III domain U-15N,13C, 20mM phosphate buffer NA, 100mM NaCl, 1mM d-DTT, 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: 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, P.structure solution
OPALpR.KORADI,M.BILLETER,P.GUNTERTrefinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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