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- EMDB-0014: Two protofilament beta-2-microglobulin amyloid fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-0014
TitleTwo protofilament beta-2-microglobulin amyloid fibril
Map dataBeta-2-microglobulin amyloid fibril - two protofilamets
Sample
  • Complex: two protofilament beta-2-microglobulin amyloid fibril
    • Protein or peptide: Beta-2-microglobulinBeta-2 microglobulin
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / 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)
Methodhelical reconstruction / cryo EM / Resolution: 3.975 Å
AuthorsIadanza MG / Ranson NA
Funding support United Kingdom, United States, 5 items
OrganizationGrant numberCountry
European Research Council322408 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)EB-002026 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AG-058504 United States
Wellcome Trust092896MA United Kingdom
Wellcome Trust204963 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: The structure of a β-microglobulin fibril suggests a molecular basis for its amyloid polymorphism.
Authors: Matthew G Iadanza / Robert Silvers / Joshua Boardman / Hugh I Smith / Theodoros K Karamanos / Galia T Debelouchina / Yongchao Su / Robert G Griffin / Neil A Ranson / Sheena E Radford /
Abstract: All amyloid fibrils contain a cross-β fold. How this structure differs in fibrils formed from proteins associated with different diseases remains unclear. Here, we combine cryo-EM and MAS-NMR to ...All amyloid fibrils contain a cross-β fold. How this structure differs in fibrils formed from proteins associated with different diseases remains unclear. Here, we combine cryo-EM and MAS-NMR to determine the structure of an amyloid fibril formed in vitro from β-microglobulin (βm), the culprit protein of dialysis-related amyloidosis. The fibril is composed of two identical protofilaments assembled from subunits that do not share βm's native tertiary fold, but are formed from similar β-strands. The fibrils share motifs with other amyloid fibrils, but also contain unique features including π-stacking interactions perpendicular to the fibril axis and an intramolecular disulfide that stabilises the subunit fold. We also describe a structural model for a second fibril morphology and show that it is built from the same subunit fold. The results provide insights into the mechanisms of fibril formation and the commonalities and differences within the amyloid fold in different protein sequences.
History
DepositionMay 18, 2018-
Header (metadata) releaseJun 20, 2018-
Map releaseNov 14, 2018-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0398
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0398
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6gk3
  • Surface level: 0.0398
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0014.png

Downloads & links

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Map

FileDownload / File: emd_0014.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBeta-2-microglobulin amyloid fibril - two protofilamets
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.0398 / Movie #1: 0.0398
Minimum - Maximum-0.08127573 - 0.13223831
Average (Standard dev.)0.000266917 (±0.0030406867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z318.000318.000318.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0810.1320.000

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Supplemental data

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Sample components

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Entire : two protofilament beta-2-microglobulin amyloid fibril

EntireName: two protofilament beta-2-microglobulin amyloid fibril
Components
  • Complex: two protofilament beta-2-microglobulin amyloid fibril
    • Protein or peptide: Beta-2-microglobulinBeta-2 microglobulin

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Supramolecule #1: two protofilament beta-2-microglobulin amyloid fibril

SupramoleculeName: two protofilament beta-2-microglobulin amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 53.3 kDa/nm

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Macromolecule #1: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.635446 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
FLNCYVSGFH PSDIEVDLLK NGERIEKVEH SDLSFSKDWS FYLLYYTEFT PTEKDEYACR VNHV

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.025 mg/mL
BufferpH: 2.5
Component:
ConcentrationFormulaName
20.0 mMCH3COONaSodium Acetate
20.0 mMNa3PO4Sodium phosphate
0.01 %NaN3Sodium Azide
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK II
DetailsQuiescent growth at 0.25 mg/ml for 5 weeks, diluted 10x with buffer

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.0032500000000000003 µm / Nominal defocus min: 0.00175 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 3-40 / Number grids imaged: 1 / Number real images: 5549 / Average exposure time: 10.0 sec. / Average electron dose: 38.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 99000 / Software - Name: RELION (ver. 2.1) / Details: 300 x 300 pixel Overlapping segments 90% overlap
CTF correctionSoftware: (Name: RELION (ver. 2.1), Gctf)
Startup modelType of model: EMDB MAP
EMDB ID:

1613


Details: Filtered to 60 Angstrom resolution
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.1)
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.83 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.608 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.975 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 11035
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6gk3:
Two protofilament beta-2-microglobulin amyloid fibril

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