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- EMDB-1229: Multiple distinct assemblies reveal conformational flexibility in... -

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Basic information

Entry
Database: EMDB / ID: EMD-1229
TitleMultiple distinct assemblies reveal conformational flexibility in the small heat shock protein Hsp26.
Map dataSurface view of the compact form of a C-terminal His-tagged variant form of yeast Hsp26
Sample
  • Sample: Hsp26, DeltaN1-30 truncation, C-terminal His tag
  • Protein or peptide: Hsp26
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.6 Å
AuthorsWhite HE / Orlova EV / Chen S / Wang L / Ignatiou A / Gowen B / Stromer T / Franzmann TM / Haslbeck M / Buchner J / Saibil HR
CitationJournal: Structure / Year: 2006
Title: Multiple distinct assemblies reveal conformational flexibility in the small heat shock protein Hsp26.
Authors: Helen E White / Elena V Orlova / Shaoxia Chen / Luchun Wang / Athanasios Ignatiou / Brent Gowen / Thusnelda Stromer / Titus M Franzmann / Martin Haslbeck / Johannes Buchner / Helen R Saibil /
Abstract: Small heat shock proteins are a superfamily of molecular chaperones that suppress protein aggregation and provide protection from cell stress. A key issue for understanding their action is to define ...Small heat shock proteins are a superfamily of molecular chaperones that suppress protein aggregation and provide protection from cell stress. A key issue for understanding their action is to define the interactions of subunit domains in these oligomeric assemblies. Cryo-electron microscopy of yeast Hsp26 reveals two distinct forms, each comprising 24 subunits arranged in a porous shell with tetrahedral symmetry. The subunits form elongated, asymmetric dimers that assemble via trimeric contacts. Modifications of both termini cause rearrangements that yield a further four assemblies. Each subunit contains an N-terminal region, a globular middle domain, the alpha-crystallin domain, and a C-terminal tail. Twelve of the C termini form 3-fold assembly contacts which are inserted into the interior of the shell, while the other 12 C termini form contacts on the surface. Hinge points between the domains allow a variety of assembly contacts, providing the flexibility required for formation of supercomplexes with non-native proteins.
History
DepositionMay 9, 2006-
Header (metadata) releaseMay 24, 2006-
Map releaseJul 25, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.034316756
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.034316756
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1229.gif

Downloads & links

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Map

FileDownload / File: emd_1229.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface view of the compact form of a C-terminal His-tagged variant form of yeast Hsp26
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.86 Å/pix.
x 128 pix.
= 238.08 Å		1.86 Å/pix.
x 128 pix.
= 238.08 Å		1.86 Å/pix.
x 128 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.86 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.00557 / Movie #1: 0.0343168
Minimum - Maximum-0.0296618 - 0.267978
Average (Standard dev.)0.00357591 (±0.0206481)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 238.08 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.861.861.86
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z238.080238.080238.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S213
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.0300.2680.004

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Supplemental data

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Sample components

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Entire : Hsp26, DeltaN1-30 truncation, C-terminal His tag

EntireName: Hsp26, DeltaN1-30 truncation, C-terminal His tag
Components
  • Sample: Hsp26, DeltaN1-30 truncation, C-terminal His tag
  • Protein or peptide: Hsp26

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Supramolecule #1000: Hsp26, DeltaN1-30 truncation, C-terminal His tag

SupramoleculeName: Hsp26, DeltaN1-30 truncation, C-terminal His tag / type: sample / ID: 1000 / Oligomeric state: 24-mer / Number unique components: 1

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Macromolecule #1: Hsp26

MacromoleculeName: Hsp26 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: 24-mer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: yeast
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.3 mg/mL
BufferpH: 7.4 / Details: 40 mM Hepes/KOH, 50 mM NaCl,
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingDigitization - Sampling interval: 1.4 µm / Number real images: 48
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: phase flipping
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Details: Angular reconstitution / Number images used: 400
Final two d classificationNumber classes: 580

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Atomic model buiding 1

Initial modelPDB ID:

1gme

SoftwareName: URO
DetailsProtocol: Rigid Body. The alpha crystallin domains were fitted manually into a the same region of density observed in the WT maps prior to refinement in URO
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT

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