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- EMDB-1614: Globular tetramers of beta-2-microglobulin assemble into elaborat... -

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Basic information

Entry
Database: EMDB / ID: EMD-1614
TitleGlobular tetramers of beta-2-microglobulin assemble into elaborate amyloid fibrils
Map dataSurface view of an B-type map from beta-2-microglobulin
Sample
  • Sample: beta-2-microglobulin
  • Protein or peptide: beta-2-microglobulin
Keywordsprotein misfolding / amyloid / cryo-EM / 3D reconstruction / STEM
Function / homologyBeta-2-Microglobulin / MHC class I protein complex
Function and homology information
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsWhite HE / Hodgkinson JL / Jahn TR / Cohen-Krausz S / Gosal WS / Muller S / Orlova EV / Radford SE / Saibil HR
CitationJournal: J Mol Biol / Year: 2009
Title: Globular tetramers of beta(2)-microglobulin assemble into elaborate amyloid fibrils.
Authors: Helen E White / Julie L Hodgkinson / Thomas R Jahn / Sara Cohen-Krausz / Walraj S Gosal / Shirley Müller / Elena V Orlova / Sheena E Radford / Helen R Saibil /
Abstract: Amyloid fibrils are ordered polymers in which constituent polypeptides adopt a non-native fold. Despite their importance in degenerative human diseases, the overall structure of amyloid fibrils ...Amyloid fibrils are ordered polymers in which constituent polypeptides adopt a non-native fold. Despite their importance in degenerative human diseases, the overall structure of amyloid fibrils remains unknown. High-resolution studies of model peptide assemblies have identified residues forming cross-beta-strands and have revealed some details of local beta-strand packing. However, little is known about the assembly contacts that define the fibril architecture. Here we present a set of three-dimensional structures of amyloid fibrils formed from full-length beta(2)-microglobulin, a 99-residue protein involved in clinical amyloidosis. Our cryo-electron microscopy maps reveal a hierarchical fibril structure built from tetrameric units of globular density, with at least three different subunit interfaces in this homopolymeric assembly. These findings suggest a more complex superstructure for amyloid than hitherto suspected and prompt a re-evaluation of the defining features of the amyloid fold.
History
DepositionApr 15, 2009-
Header (metadata) releaseApr 28, 2009-
Map releaseApr 28, 2009-
UpdateOct 20, 2009-
Current statusOct 20, 2009Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1614.tif

Downloads & links

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Map

FileDownload / File: emd_1614.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface view of an B-type map from beta-2-microglobulin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.5 Å/pix.
x 80 pix.
= 280. Å		3.5 Å/pix.
x 80 pix.
= 280. Å		3.5 Å/pix.
x 80 pix.
= 280. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-8.39024 - 21.419499999999999
Average (Standard dev.)0.00000000745257 (±2.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-39-40
Dimensions808080
Spacing808080
CellA=B=C: 280 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.53.53.5
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z280.000280.000280.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS-39-40-40
NC/NR/NS808080
D min/max/mean-8.39021.4190.000

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Supplemental data

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Sample components

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Entire : beta-2-microglobulin

EntireName: beta-2-microglobulin
Components
  • Sample: beta-2-microglobulin
  • Protein or peptide: beta-2-microglobulin

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Supramolecule #1000: beta-2-microglobulin

SupramoleculeName: beta-2-microglobulin / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 10 KDa

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Macromolecule #1: beta-2-microglobulin

MacromoleculeName: beta-2-microglobulin / type: protein_or_peptide / ID: 1 / Name.synonym: beta-2-microglobulin / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: plasma
Molecular weightExperimental: 10 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pINKWT
SequenceGO: MHC class I protein complex / InterPro: 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

Concentration0.3 mg/mL
BufferpH: 2.5 / Details: 25 mM sodium phosphate, 25 mM sodium acetate
GridDetails: holey carbon grids
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 100 K
DetailsLow dose
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 85 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 52.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 7.01 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: Maps were calculated for each class as each class had a different pitch.
CTF correctionDetails: Phase flipping

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