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- PDB-3ncm: NEURAL CELL ADHESION MOLECULE, MODULE 2, NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 3ncm
TitleNEURAL CELL ADHESION MOLECULE, MODULE 2, NMR, 20 STRUCTURES
ComponentsPROTEIN (NEURAL CELL ADHESION MOLECULE, LARGE ISOFORM)
KeywordsCELL ADHESION PROTEIN / CELL ADHESION / GLYCOPROTEIN / HEPARIN-BINDING / GPI-ANCHOR / NEURAL ADHESION MOLECULE / IMMUNOGLOBULIN FOLD / HOMOPHILIC BINDING
Function / homology
Function and homology information


regulation of exocyst assembly / NCAM1 interactions / Signal transduction by L1 / regulation of semaphorin-plexin signaling pathway / NCAM signaling for neurite out-growth / LRR domain binding / homotypic cell-cell adhesion / RAF/MAP kinase cascade / thalamus development / commissural neuron axon guidance ...regulation of exocyst assembly / NCAM1 interactions / Signal transduction by L1 / regulation of semaphorin-plexin signaling pathway / NCAM signaling for neurite out-growth / LRR domain binding / homotypic cell-cell adhesion / RAF/MAP kinase cascade / thalamus development / commissural neuron axon guidance / axonal fasciculation / negative regulation of programmed cell death / neuron development / epithelial to mesenchymal transition / multicellular organismal response to stress / phosphatase binding / positive regulation of calcium-mediated signaling / positive regulation of cardiac muscle cell proliferation / 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 / myelin sheath / heparin binding / growth cone / postsynaptic membrane / learning or memory / cell surface receptor signaling pathway / response to xenobiotic stimulus / axon / external side of plasma membrane / neuronal cell body / glutamatergic synapse / cell surface / 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 / Immunoglobulin V-Type / Fibronectin type-III domain profile. ...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 / 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
Neural cell adhesion molecule 1 / Neural cell adhesion molecule 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsJensen, P.H. / Soroka, V. / Thomsen, N.K. / Berezin, V. / Bock, E. / Poulsen, F.M.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Structure and interactions of NCAM modules 1 and 2, basic elements in neural cell adhesion
Authors: Jensen, P.H. / Soroka, V. / Thomsen, N.K. / Ralets, I. / Berezin, V. / Bock, E. / Poulsen, F.M.
History
DepositionSep 21, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list ...pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (NEURAL CELL ADHESION MOLECULE, LARGE ISOFORM)


Theoretical massNumber of molelcules
Total (without water)10,5811
Polymers10,5811
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein PROTEIN (NEURAL CELL ADHESION MOLECULE, LARGE ISOFORM) / NCAM MODULE 2


Mass: 10581.343 Da / Num. of mol.: 1 / Fragment: MODULE 2 / Mutation: K1Y, L2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: ESCHERICHIA COLI STRAIN TOP 10 F' / Plasmid: PHIL-S1 / Production host: Pichia pastoris (fungus) / Strain (production host): HIS 4 GS-115 / References: UniProt: P13594, UniProt: P13595*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
141NOESYHSQC
151TOCSYHSQC
161HSQC

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Sample preparation

DetailsContents: 10% H2O/90% D2O
Sample conditionsIonic strength: 70 mM / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.815BRUNGERrefinement
UXNMRstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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