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- PDB-1va9: Solution structure of the second FNIII domain of DSCAML1 protein -

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Basic information

Entry
Database: PDB / ID: 1va9
TitleSolution structure of the second FNIII domain of DSCAML1 protein
ComponentsDown syndrome cell adhesion molecule like-protein 1b
KeywordsCELL ADHESION / FNIII domain / DSCAML1 protein / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


dendrite self-avoidance / embryonic skeletal system morphogenesis / cell-cell adhesion mediator activity / cell fate determination / dorsal/ventral pattern formation / DSCAM interactions / homophilic cell adhesion via plasma membrane adhesion molecules / axonogenesis / central nervous system development / axon guidance ...dendrite self-avoidance / embryonic skeletal system morphogenesis / cell-cell adhesion mediator activity / cell fate determination / dorsal/ventral pattern formation / DSCAM interactions / homophilic cell adhesion via plasma membrane adhesion molecules / axonogenesis / central nervous system development / axon guidance / brain development / membrane => GO:0016020 / axon / synapse / cell surface / protein homodimerization activity / extracellular space / plasma membrane
Similarity search - Function
Cell adhesion molecule DSCAML1 / 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 ...Cell adhesion molecule DSCAML1 / 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
Down syndrome cell adhesion molecule-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQin, X.-R. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: TO BE PUBLISHED
Title: Solution structure of the second FNIII domain of DSCAML1 protein
Authors: Qin, X.-R. / Hayashi, F. / Yokoyama, S.
History
DepositionFeb 13, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2005Provider: 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: Down syndrome cell adhesion molecule like-protein 1b


Theoretical massNumber of molelcules
Total (without water)12,7551
Polymers12,7551
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 / 100
RepresentativeModel #1lowest energy

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Components

#1: Protein Down syndrome cell adhesion molecule like-protein 1b


Mass: 12754.891 Da / Num. of mol.: 1 / Fragment: FNIII domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: Kazusa cDNA KIAA1132 / Plasmid: P030623-12 / References: UniProt: Q8TD84

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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: 1.05mM 13C,15N-labeled protein; 20mM PiNa(pH6.0); 100mM NaCl; d10-DTT; 0.02% NaN3; 90% H2O; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / 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: 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
KUJIRA0.854Kobayashi,N.data analysis
CYANA1.0.7Guentert,P.structure solution
CYANA1.0.7Guentert,P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 100 / Conformers submitted total number: 20

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