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- PDB-2e8d: 3D Structure of amyloid protofilaments of beta2-microglobulin fra... -

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Basic information

Entry
Database: PDB / ID: 2e8d
Title3D Structure of amyloid protofilaments of beta2-microglobulin fragment probed by solid-state NMR
ComponentsBeta-2-microglobulinBeta-2 microglobulin
KeywordsPROTEIN FIBRIL / IMMUNE SYSTEM / beta2-microglobulin
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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...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 / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / 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 / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / 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 / membrane / identical protein binding / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR
AuthorsFujiwara, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: 3D structure of amyloid protofilaments of beta2-microglobulin fragment probed by solid-state NMR
Authors: Iwata, K. / Fujiwara, T. / Matsuki, Y. / Akutsu, H. / Takahashi, S. / Naiki, H. / Goto, Y.
History
DepositionJan 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-2-microglobulin
B: Beta-2-microglobulin
C: Beta-2-microglobulin
D: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)9,9994
Polymers9,9994
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy,target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide
Beta-2-microglobulin / Beta-2 microglobulin / K3 peptide of beta2-microglobulin


Mass: 2499.794 Da / Num. of mol.: 4 / Fragment: residues 40-61 (in UniProt numbering)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-3D-13C-13C-RFDR
1212D-3D-13C-13C-SPIN-DIFFUSION
1312D-13C-13C-SPCz5
1413D-15N-13C-SPECIFIC CP
1512D-13C-OBSERVED-1H-SPIN-DIFFUSION

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Sample preparation

DetailsContents: myloid fiber in a solid state
Sample conditionsPressure: ambient / Temperature: 245 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Infinity plusVarianInfinity plus5001
Varian Infinity plusVarianInfinity plus6002
Varian Infinity plusVarianInfinity plus7003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1refinement
SpinSight4.2Variancollection
Felix2000Accerlysprocessing
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren.structure solution
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 10

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