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- EMDB-0021: Single protofilament beta-2-microglobulin amyloid fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-0021
TitleSingle protofilament beta-2-microglobulin amyloid fibril
Map data
SampleSingle protofilament beta-2-microglobulin amyloid fibril
  • Human beta-2-microglobulinBeta-2 microglobulin
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 6.69 Å
AuthorsIadanza MG / Ranson NA
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.
DateDeposition: May 18, 2018 / Header (metadata) release: Jun 20, 2018 / Map release: May 29, 2019 / Update: May 29, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0107
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0107
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0021.png

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Map

FileDownload / File: emd_0021.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.0107 / Movie #1: 0.0107
Minimum - Maximum-0.007585158 - 0.020368278
Average (Standard dev.)0.00027549188 (±0.0018030584)
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-0.0080.0200.000

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Supplemental data

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Sample components

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Entire Single protofilament beta-2-microglobulin amyloid fibril

EntireName: Single protofilament beta-2-microglobulin amyloid fibril
Number of components: 2

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Component #1: protein, Single protofilament beta-2-microglobulin amyloid fibril

ProteinName: Single protofilament beta-2-microglobulin amyloid fibril
Recombinant expression: No
MassTheoretical: 11.7 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Human beta-2-microglobulin

ProteinName: Human beta-2-microglobulinBeta-2 microglobulin / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 4.9 Å / Delta phi: -0.639 %deg;
Sample solutionSpecimen conc.: 0.025 mg/mL / pH: 2.5
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 281.15 K / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 38.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1.75 - 3.25 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5549

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 6.69 Å / Resolution method: FSC 0.5 CUT-OFF / Details: Resolution estimated using rmeasure software

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