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- PDB-1cv9: NMR STUDY OF ITAM PEPTIDE SUBSTRATE -

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Basic information

Entry
Database: PDB / ID: 1cv9
TitleNMR STUDY OF ITAM PEPTIDE SUBSTRATE
ComponentsIG-ALPHA ITAM PEPTIDE
KeywordsIMMUNE SYSTEM / LYN TYROSINE KINASE / ITAM / IMMUNORECEPTOR TYROSINE ACTIVATION MOTIF / PEPTIDE SUBSTATE
Function / homology
Function and homology information


IgM B cell receptor complex / B cell receptor complex / CD22 mediated BCR regulation / B cell activation / B cell proliferation / multivesicular body / B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell receptor signaling pathway / transmembrane signaling receptor activity ...IgM B cell receptor complex / B cell receptor complex / CD22 mediated BCR regulation / B cell activation / B cell proliferation / multivesicular body / B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell receptor signaling pathway / transmembrane signaling receptor activity / Potential therapeutics for SARS / adaptive immune response / membrane raft / external side of plasma membrane / identical protein binding / plasma membrane
Similarity search - Function
B-cell antigen receptor complex-associated protein alpha/beta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype ...B-cell antigen receptor complex-associated protein alpha/beta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
B-cell antigen receptor complex-associated protein alpha chain
Similarity search - Component
MethodSOLUTION NMR / THE SIMULATED ANNEALING PROTOCOL IN THE X-PLOR 3.1 MANUAL WAS USED FOR STRUCTURE CALCULATION. RESTRAINED POWELL MINIMIZATION INCOPORATED THE CHARMM FORCE FIELD USING THE TOP_ALL22, PAR_ALL22 FILES IN THE X-PLOR 3.1 LIBRARY. 107 NOE DERIVED DISTANCE RESTRAINTS WERE USED THROUGH OUT THE STRUCTURE CALCULATION
AuthorsGaul, B.S. / Harrison, M.L. / Geahlen, R.L. / Post, C.B.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Substrate recognition by the Lyn protein-tyrosine kinase. NMR structure of the immunoreceptor tyrosine-based activation motif signaling region of the B cell antigen receptor.
Authors: Gaul, B.S. / Harrison, M.L. / Geahlen, R.L. / Burton, R.A. / Post, C.B.
History
DepositionAug 23, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IG-ALPHA ITAM PEPTIDE


Theoretical massNumber of molelcules
Total (without water)1,4331
Polymers1,4331
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)1 / 200structures with favorable non-bond energy
Representativeclosest to the average

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Components

#1: Protein/peptide IG-ALPHA ITAM PEPTIDE


Mass: 1433.456 Da / Num. of mol.: 1 / Fragment: RESIDUES 178-189 / Source method: obtained synthetically / Details: SEQUENCE FROM HUMAN IG-ALPHA ITAM / References: UniProt: P11912*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1312D ROESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

DetailsContents: 1 MM ITP WITH 0.2 MM KLYN, PH 7.0 PHOSPHATE BUFFER
Sample conditionspH: 7.0 / Pressure: AMBIENT / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY6001
Varian UNITYVarianUNITY5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGER, A.T.structure solution
CHARMM23.2BROOKS, B.R. ET AL.refinement
RefinementMethod: THE SIMULATED ANNEALING PROTOCOL IN THE X-PLOR 3.1 MANUAL WAS USED FOR STRUCTURE CALCULATION. RESTRAINED POWELL MINIMIZATION INCOPORATED THE CHARMM FORCE FIELD USING THE TOP_ALL22, PAR_ALL22 ...Method: THE SIMULATED ANNEALING PROTOCOL IN THE X-PLOR 3.1 MANUAL WAS USED FOR STRUCTURE CALCULATION. RESTRAINED POWELL MINIMIZATION INCOPORATED THE CHARMM FORCE FIELD USING THE TOP_ALL22, PAR_ALL22 FILES IN THE X-PLOR 3.1 LIBRARY. 107 NOE DERIVED DISTANCE RESTRAINTS WERE USED THROUGH OUT THE STRUCTURE CALCULATION
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 200 / Conformers submitted total number: 1

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