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- PDB-1jnj: NMR solution structure of the human beta2-microglobulin -

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Basic information

Entry
Database: PDB / ID: 1jnj
TitleNMR solution structure of the human beta2-microglobulin
Componentsbeta2-microglobulin
KeywordsIMMUNE SYSTEM / immunoglobulin constant domain
Function / homology
Function and homology information


negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / 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 ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, restrained molecular dynamics, restrained molecular mechanics
AuthorsVerdone, G. / Corazza, A. / Viglino, P. / Pettirossi, F. / Giorgetti, S. / Mangione, P. / Andreola, A. / Stoppini, M. / Bellotti, V. / Esposito, G.
Citation
Journal: Protein Sci. / Year: 2002
Title: The solution structure of human beta2-microglobulin reveals the prodromes of its amyloid transition.
Authors: Verdone, G. / Corazza, A. / Viglino, P. / Pettirossi, F. / Giorgetti, S. / Mangione, P. / Andreola, A. / Stoppini, M. / Bellotti, V. / Esposito, G.
#1: Journal: Protein Sci. / Year: 2000
Title: Removal of the N-terminal hexapeptide from human beta2-microglobulin facilitates protein aggregation and fibril formation
Authors: Esposito, G. / Michelutti, R. / Verdone, G. / Viglino, P. / Hernandez, H. / Robinson, C.V. / Amoresano, A. / Dal Piaz, F. / Monti, M. / Pucci, P. / Mangione, P. / Stoppini, M. / Merlini, G. ...Authors: Esposito, G. / Michelutti, R. / Verdone, G. / Viglino, P. / Hernandez, H. / Robinson, C.V. / Amoresano, A. / Dal Piaz, F. / Monti, M. / Pucci, P. / Mangione, P. / Stoppini, M. / Merlini, G. / Ferri, G. / Bellotti, V.
#2: Journal: Eur.J.Biochem. / Year: 1998
Title: Beta2-microglobulin can be refolded into a native state from ex vivo amyloid fibrils.
Authors: Bellotti, V. / Stoppini, M. / Mangione, P. / Sunde, M. / Robinson, C.V. / Asti, L. / Brancaccio, D. / Ferri, G.
History
DepositionJul 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta2-microglobulin


Theoretical massNumber of molelcules
Total (without water)11,8791
Polymers11,8791
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 / 380target function
Representative

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Components

#1: Protein beta2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pHN1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P61769
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
10.68 mM beta2-m; 70 mM phosphate buffer NA, 100 mM NaCl.90% H2O/10% D2O
20.37 mM beta2-m; 70 mM phosphate buffer NA, 100 mM NaCl.100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl, 70 mM phosphate buffer 6.4ambient 310 K
2100 mM NaCl, 70 mM phosphate buffer 6.4ambient 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
Felix2000MSIprocessing
Felix2000MSIdata analysis
DIANA1.5Guentertstructure solution
Discover2000MSIrefinement
RefinementMethod: simulated annealing, restrained molecular dynamics, restrained molecular mechanics
Software ordinal: 1
Details: the structures are based on a total of 1608 restraints, 1541 are NOE-derived distance contraints, 67 dihedral angle restraints
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 380 / Conformers submitted total number: 20

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