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- PDB-1uem: Solution Structure of the First Fibronectin Type III domain of hu... -

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Basic information

Entry
Database: PDB / ID: 1uem
TitleSolution Structure of the First Fibronectin Type III domain of human KIAA1568 Protein
ComponentsKIAA1568 Protein
Keywordsstructural genomics / unknown function / Immunoglobulin-like beta-sandwich fold / fibronectin type III / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


olfactory bulb interneuron development / apoptotic process involved in luteolysis / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of synapse assembly / heart induction / ROBO receptors bind AKAP5 / axon guidance receptor activity / Formation of the ureteric bud / Regulation of commissural axon pathfinding by SLIT and ROBO ...olfactory bulb interneuron development / apoptotic process involved in luteolysis / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of synapse assembly / heart induction / ROBO receptors bind AKAP5 / axon guidance receptor activity / Formation of the ureteric bud / Regulation of commissural axon pathfinding by SLIT and ROBO / outflow tract septum morphogenesis / endocardial cushion formation / Signaling by ROBO receptors / pulmonary valve morphogenesis / metanephros development / aortic valve morphogenesis / axon midline choice point recognition / aorta development / ureteric bud development / positive regulation of axonogenesis / ventricular septum morphogenesis / retinal ganglion cell axon guidance / positive regulation of Notch signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / axolemma / cellular response to hormone stimulus / axon guidance / central nervous system development / brain development / cell-cell adhesion / Regulation of expression of SLITs and ROBOs / chemotaxis / cell surface / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III ...Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Roundabout homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsLi, H. / Kigawa, T. / Tochio, N. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of the First Fibronectin Type III domain of human KIAA1568 Protein
Authors: Li, H. / Kigawa, T. / Tochio, N. / Koshiba, S. / 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_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
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KIAA1568 Protein


Theoretical massNumber of molelcules
Total (without water)12,3621
Polymers12,3621
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 #1lowest energy

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Components

#1: Protein KIAA1568 Protein


Mass: 12361.629 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 fh22308 / Plasmid: P021007-51 / References: UniProt: Q9HCK4

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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: 1.1mM fibronectin type III domain 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: 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
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.811Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
OPALpR. Koradi, M. Billeter, P. Guentertrefinement
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,structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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