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- PDB-5lkn: NMR solution structure of human FNIII domain 2 of NCAM -

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Basic information

Entry
Database: PDB / ID: 5lkn
TitleNMR solution structure of human FNIII domain 2 of NCAM
ComponentsNeural cell adhesion molecule 1
KeywordsCELL ADHESION / fibronectin type III domain / protein interactions
Function / homology
Function and homology information


regulation of semaphorin-plexin signaling pathway / commissural neuron axon guidance / NCAM1 interactions / ECM proteoglycans / epithelial to mesenchymal transition / NCAM signaling for neurite out-growth / Signal transduction by L1 / Interferon gamma signaling / virus receptor activity / RAF/MAP kinase cascade ...regulation of semaphorin-plexin signaling pathway / commissural neuron axon guidance / NCAM1 interactions / ECM proteoglycans / epithelial to mesenchymal transition / NCAM signaling for neurite out-growth / Signal transduction by L1 / Interferon gamma signaling / virus receptor activity / RAF/MAP kinase cascade / collagen-containing extracellular matrix / cell adhesion / external side of plasma membrane / Golgi membrane / cell surface / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Neural cell adhesion / 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 ...Neural cell adhesion / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neural cell adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSlapsak, U. / Salzano, G. / Amin, L. / Abskharon, R.N.N. / Ilc, G. / Zupancic, B. / Biljan, I. / Plavec, J. / Giachin, G. / Legname, G.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-242 Slovenia
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The N Terminus of the Prion Protein Mediates Functional Interactions with the Neuronal Cell Adhesion Molecule (NCAM) Fibronectin Domain.
Authors: Slapsak, U. / Salzano, G. / Amin, L. / Abskharon, R.N. / Ilc, G. / Zupancic, B. / Biljan, I. / Plavec, J. / Giachin, G. / Legname, G.
History
DepositionJul 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neural cell adhesion molecule 1


Theoretical massNumber of molelcules
Total (without water)11,8581
Polymers11,8581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6670 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Neural cell adhesion molecule 1 / NCAM-1


Mass: 11858.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Details about the sequence Residue at position 595 is methionine and was added for the beginning of translation Residues 692-697 on C-terminal represents six histidine residues which were ...Details: Details about the sequence Residue at position 595 is methionine and was added for the beginning of translation Residues 692-697 on C-terminal represents six histidine residues which were used as His-tag for protein purification
Source: (gene. exp.) Homo sapiens (human) / Gene: NCAM1, NCAM / Plasmid: pET11a / Cell (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P13591

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CO)CA
1121isotropic13D HNCA
1111isotropic13D CBCA(CO)NH
1101isotropic13D HN(CA)CB
191isotropic13D HBHA(CO)NH
181isotropic13D CC(CO)NH
171isotropic13D (H)CCH-TOCSY
161isotropic13D 1H-15N NOESY
1141isotropic13D 1H-13C NOESY aliphatic
1131isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.9 mM [U-99% 13C; U-99% 15N] "fibronectin type III domain 2, 20 mM TBS, 150 mM sodium chloride, 10 % [U-2H] D2O, 90 % H2O, 90% H2O/10% D2O
Label: 13C and 15N labelled / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mM"fibronectin type III domain 2[U-99% 13C; U-99% 15N]1
20 mMTBSnatural abundance1
150 mMsodium chloridenatural abundance1
10 %D2O[U-2H]1
90 %H2Onatural abundance1
Sample conditionsIonic strength: 150 mM / Label: 13C and 15N labelled / pH: 7.45 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAv1.8.42Keller and Wuthrichchemical shift assignment
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
YASARAElmar Krieger and Gert Vriendrefinement
CINGDoreleijers JFdata analysis
PSVSBhattacharya and Montelionedata analysis
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
RefinementMethod: simulated annealing / Software ordinal: 4 / Details: water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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