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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-microglobulin
Keywordsamyloid / b2m / PROTEIN FIBRIL
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 / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...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 / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / 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 / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma 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 / 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 / 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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 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 °

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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-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)
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

UniProtKB: Beta-2-microglobulin

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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 / Pretreatment - Time: 60 sec.
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
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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
Segment selectionNumber selected: 99000 / Software - Name: RELION (ver. 2.1) / Details: 300 x 300 pixel Overlapping segments 90% overlap
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)
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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