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- PDB-2vb5: Solution structure of W60G mutant of human beta2-microglobulin -

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Basic information

Entry
Database: PDB / ID: 2vb5
TitleSolution structure of W60G mutant of human beta2-microglobulin
ComponentsBETA-2-MICROGLOBULIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN CONSTANT DOMAIN / AMYLOID DISEASE / IMMUNE RESPONSE / MHC I / SECRETED / GLYCATION / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / ER-Phagosome pathway / iron ion transport / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Beta-2-Microglobulin / 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 ...Beta-2-Microglobulin / 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
Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsEsposito, G. / Corazza, A. / Rennella, E. / Gumral, D. / Mimmi, M.C. / Fogolari, F. / Viglino, P. / Raimondi, S. / Giorgetti, S. / Bolognesi, B. ...Esposito, G. / Corazza, A. / Rennella, E. / Gumral, D. / Mimmi, M.C. / Fogolari, F. / Viglino, P. / Raimondi, S. / Giorgetti, S. / Bolognesi, B. / Merlini, G. / Stoppini, M. / Bellotti, V.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Controlling Roles of Trp60 and Trp95 in Beta2-Microglobulin Function, Folding and Amyloid Aggregation Properties.
Authors: Esposito, G. / Ricagno, S. / Corazza, A. / Rennella, E. / Gumral, D. / Mimmi, M.C. / Betto, E. / Pucillo, C.E.M. / Fogolari, F. / Viglino, P. / Raimondi, S. / Giorgetti, S. / Bolognesi, B. / ...Authors: Esposito, G. / Ricagno, S. / Corazza, A. / Rennella, E. / Gumral, D. / Mimmi, M.C. / Betto, E. / Pucillo, C.E.M. / Fogolari, F. / Viglino, P. / Raimondi, S. / Giorgetti, S. / Bolognesi, B. / Merlini, G. / Stoppini, M. / Bolognesi, M. / Bellotti, V.
History
DepositionSep 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr ..._pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-2-MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)11,7501
Polymers11,7501
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 / 300LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein BETA-2-MICROGLOBULIN


Mass: 11750.198 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P61769
Compound detailsENGINEERED RESIDUE IN CHAIN A, TRP 80 TO GLY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121NOESY
131DQF-COSY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 95% WATER/5% D2O
Sample conditionsIonic strength: 100 mM / pH: 6.6 / Pressure: 1.0 atm / Temperature: 310.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Discover2000MSIrefinement
Felixstructure solution
CYANAstructure solution
Discoverstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 300 / Conformers submitted total number: 20

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