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- PDB-1ie5: NMR STRUCTURE OF THE THIRD IMMUNOGLOBULIN DOMAIN FROM THE NEURAL ... -

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Basic information

Entry
Database: PDB / ID: 1ie5
TitleNMR STRUCTURE OF THE THIRD IMMUNOGLOBULIN DOMAIN FROM THE NEURAL CELL ADHESION MOLECULE.
ComponentsNEURAL CELL ADHESION MOLECULE
KeywordsCELL ADHESION / Intermediate Immunoglobulin fold
Function / homology
Function and homology information


synaptic membrane adhesion / homophilic cell adhesion via plasma membrane adhesion molecules / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Neural cell adhesion molecule 1 / Neural cell adhesion / 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 molecule 1 / Neural cell adhesion / 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 speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing restrained molecular dynamics
AuthorsAtkins, A.R. / Chung, J. / Deechongkit, S. / Little, E.B. / Edelman, G.M. / Wright, P.E. / Cunningham, B.A. / Dyson, H.J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Solution structure of the third immunoglobulin domain of the neural cell adhesion molecule N-CAM: can solution studies define the mechanism of homophilic binding?
Authors: Atkins, A.R. / Chung, J. / Deechongkit, S. / Little, E.B. / Edelman, G.M. / Wright, P.E. / Cunningham, B.A. / Dyson, H.J.
History
DepositionApr 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Remark 999SEQUENCE THE PROTEIN IS A FRAGMENT CONSISTING OF THE THIRD IMMUNOGLOBULIN DOMAIN. The residue ...SEQUENCE THE PROTEIN IS A FRAGMENT CONSISTING OF THE THIRD IMMUNOGLOBULIN DOMAIN. The residue numbers that are referred to (183-288) are for the processed protein, after removal of the signal sequence. The signal sequence is included in the SwissProt database, hence the discrepancy in the numbering. The correct match with the database numbering is with residues 202 -307, with an additional N-terminal glycine introducing in the cloning.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURAL CELL ADHESION MOLECULE


Theoretical massNumber of molelcules
Total (without water)11,8511
Polymers11,8511
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 / 200structures with the least restraint violations
RepresentativeModel #6

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Components

#1: Protein NEURAL CELL ADHESION MOLECULE / N-CAM


Mass: 11851.091 Da / Num. of mol.: 1 / Fragment: THIRD IMMUNOGLOBULIN DOMAIN, RESIDUES 183-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Organ: BRAIN / Plasmid: PET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13590

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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
131HNHB
141CGCN, CGCO
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 1mM IgIII U-15N,13C; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: no salt / pH: 6.8 / Pressure: ambient / 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: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8Delaglioprocessing
DYANA1.5Guentertstructure solution
Amber7Caserefinement
NMRView3Johnsondata analysis
SANE1Duggandata analysis
RefinementMethod: simulated annealing restrained molecular dynamics / Software ordinal: 1
Details: The structure is based on 1461 unique NOE-derived restraints, 393 ambiguous NOE-derived restraints, and 131 dihedral angle restraints.
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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