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- PDB-2xks: Prion-like conversion during amyloid formation at atomic resolution -

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Basic information

Entry
Database: PDB / ID: 2xks
TitlePrion-like conversion during amyloid formation at atomic resolution
ComponentsBETA-2-MICROGLOBULIN
KeywordsIMMUNE SYSTEM / AMYLOIDOSIS / IG-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
AuthorsEichner, T. / Kalverda, A.P. / Thompson, G.S. / Radford, S.E. / Homans, S.W.
Citation
Journal: Mol.Cell / Year: 2011
Title: Conformational Conversion During Amyloid Formation at Atomic Resolution.
Authors: Eichner, T. / Kalverda, A.P. / Thompson, G.S. / Homans, S.W. / Radford, S.E.
#1: Journal: J.Mol.Biol. / Year: 2009
Title: A Generic Mechanism of Beta2-Microglobulin Amyloid Assembly at Neutral Ph Involving a Specific Proline Switch.
Authors: Eichner, T. / Radford, S.E.
History
DepositionJul 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.page_last / _pdbx_nmr_spectrometer.field_strength ..._citation.page_last / _pdbx_nmr_spectrometer.field_strength / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.4Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)11,7481
Polymers11,7481
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)30 / 30LOWEST ENERGY
Representative

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Components

#1: Protein BETA-2-MICROGLOBULIN


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET23A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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
111CBCA(CO)NH
121C(CO)NH
131H(CCO)NH
141HNCA
151HNCO
161HN(CO)CA
171N15 HSQC
181C TOCSY
191HN(CA)CB
1101H COSY
1111H TOCSY
1121N15 NOESY
1131C13 ARO HSQC
1141C13 HSQC
1151(HB)CB(CGCD)HD
1161C13 ARO NOESY
1171C13 NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED BETA-2-MICROGLOBULIN

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Sample preparation

Details
Solution-IDContents
190% H2O/10% D2O
2100% D2O
Sample conditionsIonic strength: 0.04 / pH: 7.5 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis1CCPNrefinement
PASD ALGORITHM1structure solution
NMRView5.22structure solution
NMRPipe2.5structure solution
ARIA2.1structure solution
CcpNmr Analysis2.1structure solution
Xplor-NIH2.17structure solution
VNMR6.1Cstructure solution
RefinementSoftware ordinal: 1
Details: THE CCPN NMR ASSIGNMENT AND DATA ANALYSIS APPLICATION.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 30 / Conformers submitted total number: 30

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