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- PDB-1f3r: COMPLEX BETWEEN FV ANTIBODY FRAGMENT AND AN ANALOGUE OF THE MAIN ... -

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Basic information

Entry
Database: PDB / ID: 1f3r
TitleCOMPLEX BETWEEN FV ANTIBODY FRAGMENT AND AN ANALOGUE OF THE MAIN IMMUNOGENIC REGION OF THE ACETYLCHOLINE RECEPTOR
Components
  • ACETYLCHOLINE RECEPTOR ALPHA
  • FV ANTIBODY FRAGMENT
KeywordsIMMUNE SYSTEM / IG-FOLD / IMMUNO COMPLEX / ANTIBODY-ANTIGEN / BETA-TURN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / : / :
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / distance geometry simulated annealing docking molecular dynamics
AuthorsKleinjung, J. / Petit, M.-C. / Orlewski, P. / Mamalaki, A. / Tzartos, S.-J. / Tsikaris, V. / Sakarellos-Daitsiotis, M. / Sakarellos, C. / Marraud, M. / Cung, M.-T.
CitationJournal: Biopolymers / Year: 2000
Title: The third-dimensional structure of the complex between an Fv antibody fragment and an analogue of the main immunogenic region of the acetylcholine receptor: a combined two-dimensional NMR, ...Title: The third-dimensional structure of the complex between an Fv antibody fragment and an analogue of the main immunogenic region of the acetylcholine receptor: a combined two-dimensional NMR, homology, and molecular modeling approach.
Authors: Kleinjung, J. / Petit, M.C. / Orlewski, P. / Mamalaki, A. / Tzartos, S.J. / Tsikaris, V. / Sakarellos-Daitsiotis, M. / Sakarellos, C. / Marraud, M. / Cung, M.T.
History
DepositionJun 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLCHOLINE RECEPTOR ALPHA
B: FV ANTIBODY FRAGMENT


Theoretical massNumber of molelcules
Total (without water)28,8672
Polymers28,8672
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ACETYLCHOLINE RECEPTOR ALPHA


Mass: 1091.175 Da / Num. of mol.: 1 / Fragment: MAIN IMMUNOGENIC REGION (91-100) / Mutation: A70G, K76NLE / Source method: obtained synthetically
Details: Sequence is derived from acetylcholine receptor of Torpedo electric organ
References: GenBank: 223528
#2: Antibody FV ANTIBODY FRAGMENT


Mass: 27775.750 Da / Num. of mol.: 1
Fragment: FRAGMENT OF MAB198 RAISED AGAINST HUMAN ACETYLCHOLINE RECEPTOR
Source method: isolated from a natural source
Details: MONOCLONAL ANTIBODY(MAB198) RAISED AGAINST HUMAN ACETYLCHOLINE RECEPTOR
Source: (natural) Rattus norvegicus (Norway rat) / References: GenBank: 404506, GenBank: 404508

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 0.2 mM mAb198, 10 mM MIR peptide antigen, 0.1 M phosphate buffer
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.1 M / pH: 7.2 / Pressure: ambient / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR940501.3Brukerprocessing
XEASY1.3Xia, Bartelsdata analysis
DYANA1.2Guentert, Mumenthaler, Herrmannstructure solution
DISCOVER397MSIrefinement
RefinementMethod: distance geometry simulated annealing docking molecular dynamics
Software ordinal: 1
Details: The peptide structure is based on 73 NOE-derived distance restraints. The antibody structure is based on template structures Pot IgM and Fab D1.3 antilysozyme. The complex structure has been ...Details: The peptide structure is based on 73 NOE-derived distance restraints. The antibody structure is based on template structures Pot IgM and Fab D1.3 antilysozyme. The complex structure has been derived by computational docking.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 1 / Conformers submitted total number: 1

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