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

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Basic information

Entry
Database: PDB / ID: 2xku
TitlePrion-like conversion during amyloid formation at atomic resolution
ComponentsBETA-2-MICROGLOBULINBeta-2 microglobulin
KeywordsIMMUNE SYSTEM / AMYLOIDOSIS / IG-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 / 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 / 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
AuthorsEichner, T. / Kalverda, A.P. / Thompson, G.S. / Homans, S.W. / Radford, S.E.
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 9, 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 1.5Jun 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 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-2-MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)11,1531
Polymers11,1531
Non-polymers00
Water0
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 / Beta-2 microglobulin / BETA-2-MICROGLOBULIN FORM PI 5.3 / DN6


Mass: 11153.478 Da / Num. of mol.: 1 / Fragment: IMMUNGLOBULIN, RESIDUES 27-119
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
Sequence detailsDELTA-N-6, 5-MET

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115NNOESY CORR
221HNCA
331HN(CA)CB
441HSQC
551D2O AROCHSQC
661(H)CCH ARO
771CBCA(CO)NH
881C TOCSY
991HNCO
10101HN(CO)CA
11111(H)CCH TOCSY
12121(H)CCH COSY
13131HDA
14141HEA
15151AROCNOESY
16161D2O CHSQC
17171D2O CNOESY
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 conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.04 7.5 1.0 atm298.0 K
20.04 7.5 1.0 atm298.0 K
30.04 7.5 1.0 atm298.0 K
40.04 7.5 1.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA7504

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis1CCPNrefinement
CcpNmr Analysis2.1structure solution
Xplor-NIH2.17structure solution
NMRPipe2.5structure solution
ARIA2.1structure solution
NMRView5.22structure solution
PASD ALGORITHM1structure 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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