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- PDB-4ba8: High resolution NMR structure of the C mu3 domain from IgM -

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Basic information

Entry
Database: PDB / ID: 4ba8
TitleHigh resolution NMR structure of the C mu3 domain from IgM
ComponentsIG MU CHAIN C REGION SECRETED FORM
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN CONSTANT REGION
Function / homology
Function and homology information


CD22 mediated BCR regulation / hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / pre-B cell allelic exclusion / Cell surface interactions at the vascular wall / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of B cell activation / B cell affinity maturation ...CD22 mediated BCR regulation / hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / pre-B cell allelic exclusion / Cell surface interactions at the vascular wall / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of B cell activation / B cell affinity maturation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / regulation of cell morphogenesis / regulation of immunoglobulin production / positive regulation of endocytosis / B cell activation / immunoglobulin complex, circulating / B cell proliferation / immunoglobulin receptor binding / immunoglobulin mediated immune response / antigen processing and presentation / complement activation, classical pathway / positive regulation of B cell proliferation / antigen binding / B cell receptor signaling pathway / positive regulation of immune response / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / antibacterial humoral response / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / adaptive immune response / external side of plasma membrane / innate immune response / perinuclear region of cytoplasm / cell surface / extracellular space / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant mu
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR / ARIA
AuthorsMueller, R. / Kern, T. / Graewert, M.A. / Madl, T. / Peschek, J. / Groll, M. / Sattler, M. / Buchner, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: High Resolution Structures of the Igm Fc Domains Reveal Principles of its Hexamer Formation
Authors: Mueller, R. / Graewert, M.A. / Kern, T. / Madl, T. / Peschek, J. / Sattler, M. / Groll, M. / Buchner, J.
History
DepositionSep 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 2.0Jun 14, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IG MU CHAIN C REGION SECRETED FORM


Theoretical massNumber of molelcules
Total (without water)11,2631
Polymers11,2631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein IG MU CHAIN C REGION SECRETED FORM / IMMUNOGLOBULIN M


Mass: 11262.790 Da / Num. of mol.: 1 / Fragment: C MU3, RESIDUES 222-321 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01872

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N HSQC
12113C HSQC
13115N NOESY
14113C NOESY ALIPHATICS
15113C NOESY AROMATICS
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% H20/10% D20, 20MM PHOSHATE BUFFER, 50MM NACL
Sample conditionsIonic strength: 50 mM / pH: 6.8 / Temperature: 298.0 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNS-ARIABRUNGER, ADAMS,CLORE,GROS,NILGES,READrefinement
CNS-ARIAstructure solution
CYANAstructure solution
NMRPipestructure solution
Sparkystructure solution
CcpNmr Analysis2structure solution
RefinementMethod: ARIA / Software ordinal: 1
Details: DISTANCE RESTRAINTS DERIVED FROM FROM TALOS BASED ON SECONDARY CHEMICAL SHIFTS, AND RDC RESTRAINTS WERE APPLIED FOR A WATER REFINEMENT CALCULATION USING A SIMULATED ANNEALING PROTOCOL IN CNS.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers submitted total number: 20

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