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- EMDB-0019: Four protofilament beta-2-microglobulin amyloid fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-0019
TitleFour protofilament beta-2-microglobulin amyloid fibril
Map dataFour protofilament beta-2-microglobulin amyloid fibril
Sample
  • Complex: four protofilament beta-2-microglobulin amyloid fibril
    • Protein or peptide: Human beta-2-microglobulinBeta-2 microglobulin
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 9.42 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 SciencesAG-058504 United States
National Institutes of Health/National Institute of General Medical SciencesEB-002026 United States
Wellcome Trust204963 United Kingdom
Wellcome Trust092896MA 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 releaseJun 19, 2019-
UpdateJan 15, 2020-
Current statusJan 15, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0089
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0089
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0019.png

Downloads & links

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Map

FileDownload / File: emd_0019.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFour protofilament beta-2-microglobulin amyloid fibril
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.0089 / Movie #1: 0.0089
Minimum - Maximum-0.005038559 - 0.019340014
Average (Standard dev.)0.00028363764 (±0.0018114602)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 635.99994 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z636.000636.000636.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0050.0190.000

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Supplemental data

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Sample components

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Entire : four protofilament beta-2-microglobulin amyloid fibril

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

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

SupramoleculeName: four 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: 11.7 KDa

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Macromolecule #1: Human beta-2-microglobulin

MacromoleculeName: Human beta-2-microglobulin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
IQRTPKIQVY SRHPAENGKS NFLNCYVSGF HPSDIEVDLL KNGERIEKVE HSDLSFSKDW SFYLLYYTE FTPTEKDEYA CRVNHVTLSQ PKIVKWDRDM

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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: 0.00325 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

CTF correctionSoftware: (Name: RELION (ver. 2.1), Gctf)
Startup modelType of model: OTHER
Details: Double protofilament map from same study 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: 2.3 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.161 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.42 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Details: Resolution estimated using rmeasure software / Number images used: 8891

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