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- PDB-1lwr: Solution structure of the NCAM fibronectin type III module 2 -

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Basic information

Entry
Database: PDB / ID: 1lwr
TitleSolution structure of the NCAM fibronectin type III module 2
ComponentsNeural Cell Adhesion Molecule 1, 140 kDa isoform
KeywordsCELL ADHESION / All beta / Fibronectin type III module
Function / homology
Function and homology information


NCAM1 interactions / regulation of exocyst assembly / regulation of semaphorin-plexin signaling pathway / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / cellular response to molecule of bacterial origin / peripheral nervous system axon regeneration / LRR domain binding / homotypic cell-cell adhesion / NCAM signaling for neurite out-growth / Signal transduction by L1 ...NCAM1 interactions / regulation of exocyst assembly / regulation of semaphorin-plexin signaling pathway / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / cellular response to molecule of bacterial origin / peripheral nervous system axon regeneration / LRR domain binding / homotypic cell-cell adhesion / NCAM signaling for neurite out-growth / Signal transduction by L1 / cellular response to inorganic substance / thalamus development / fibroblast growth factor receptor binding / commissural neuron axon guidance / axonal fasciculation / negative regulation of programmed cell death / RAF/MAP kinase cascade / response to inorganic substance / neuron development / epithelial to mesenchymal transition / multicellular organismal response to stress / phosphatase binding / animal organ regeneration / positive regulation of calcium-mediated signaling / positive regulation of cardiac muscle cell proliferation / cytoskeletal protein binding / response to activity / response to cocaine / calcium-mediated signaling / response to lead ion / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron projection development / cell-cell junction / presynaptic membrane / heparin binding / growth cone / postsynaptic membrane / learning or memory / cell surface receptor signaling pathway / cell adhesion / response to xenobiotic stimulus / axon / external side of plasma membrane / neuronal cell body / glutamatergic synapse / cell surface / plasma membrane
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 speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / distance geometry; simulated annealing
AuthorsKiselyov, V.V. / Skladchikova, G. / Hinsby, A.M. / Jensen, P.H. / Kulahin, N. / Pedersen, N. / Tsetlin, V. / Poulsen, F.M. / Berezin, V. / Bock, E.
CitationJournal: Structure / Year: 2003
Title: Structural basis for a direct interaction between FGFR1 and NCAM and evidence for a regulatory role of ATP
Authors: Kiselyov, V.V. / Skladchikova, G. / Hinsby, A.M. / Jensen, P.H. / Kulahin, N. / Soroka, V. / Pedersen, N. / Tsetlin, V. / Poulsen, F.M. / Berezin, V. / Bock, E.
History
DepositionJun 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: 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: Neural Cell Adhesion Molecule 1, 140 kDa isoform


Theoretical massNumber of molelcules
Total (without water)10,6581
Polymers10,6581
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)30 / 78Z-scores less than 2.4
RepresentativeModel #4lowest energy

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Components

#1: Protein Neural Cell Adhesion Molecule 1, 140 kDa isoform / / NCAM / NCAM polypeptide / N-CAM 140 / NCAM-140


Mass: 10657.956 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ncam1 / Plasmid: pPICZa / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: P13596

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
142DQF-COSY
1522D NOESY
1622D TOCSY
1733D 15N-separated NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques and triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM NCAM FnIII module 2 unlabelled; 30 mM NaCl, 10 mM sodium phosphate, pH 7.2790% H2O/10% D2O
22mM NCAM FnIII module 2 unlabelled; 30 mM NaCl, 10 mM sodium phosphate, pH 7.27100% D2O
31mM NCAM FnIII module 2 U-15N; 30 mM NaCl, 10 mM sodium phosphate, pH 7.2790% H2O/10% D2O
Sample conditionsIonic strength: 40 mM / pH: 7.27 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Pronto19981230Kjaer. M.data analysis
MNMRKjaer. M.processing
X-PLOR3.1Brunger, A.refinement
RefinementMethod: distance geometry; simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Z-scores less than 2.4 / Conformers calculated total number: 78 / Conformers submitted total number: 30

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