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- EMDB-1979: Structural Dynamics of Archaeal Small Heat Shock Proteins -

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Basic information

Entry
Database: EMDB / ID: EMD-1979
TitleStructural Dynamics of Archaeal Small Heat Shock Proteins
Map dataSmall Hsp16.5 assembly
Sample
  • Sample: Hsp16.5 from Methanocaldococcus jannaschii
  • Protein or peptide: Small Heat Shock Protein
Function / homologyAlpha crystallin/Hsp20 domain / response to stress
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
Methodsingle particle reconstruction / negative staining / Resolution: 19.0 Å
AuthorsHaslbeck M / Kastenmueller A / Buchner J / Weinkauf S / Braun N
CitationJournal: J Mol Biol / Year: 2008
Title: Structural dynamics of archaeal small heat shock proteins.
Authors: Martin Haslbeck / Andreas Kastenmüller / Johannes Buchner / Sevil Weinkauf / Nathalie Braun /
Abstract: Small heat shock proteins (sHsps) are a widespread and diverse class of molecular chaperones. In vivo, sHsps contribute to thermotolerance. Recent evidence suggests that their function in the ...Small heat shock proteins (sHsps) are a widespread and diverse class of molecular chaperones. In vivo, sHsps contribute to thermotolerance. Recent evidence suggests that their function in the cellular chaperone network is to maintain protein homeostasis by complexing a variety of non-native proteins. One of the most characteristic features of sHsps is their organization into large, sphere-like structures commonly consisting of 12 or 24 subunits. Here, we investigated the functional and structural properties of Hsp20.2, an sHsp from Archaeoglobus fulgidus, in comparison to its relative, Hsp16.5 from Methanocaldococcus jannaschii. Hsp20.2 is active in suppressing the aggregation of different model substrates at physiological and heat-stress temperatures. Electron microscopy showed that Hsp20.2 forms two distinct types of octahedral oligomers of slightly different sizes, indicating certain structural flexibility of the oligomeric assembly. By three-dimensional analysis of electron microscopic images of negatively stained specimens, we were able to reconstitute 3D models of the assemblies at a resolution of 19 A. Under conditions of heat stress, the distribution of the structurally different Hsp20.2 assemblies changed, and this change was correlated with an increased chaperone activity. In analogy to Hsp20.2, Hsp16.5 oligomers displayed structural dynamics and exhibited increased chaperone activity under conditions of heat stress. Thus, temperature-induced conformational regulation of the activity of sHsps may be a general phenomenon in thermophilic archaea.
History
DepositionNov 2, 2011-
Header (metadata) releaseNov 25, 2011-
Map releaseNov 25, 2011-
UpdateNov 25, 2011-
Current statusNov 25, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Hsp16.5_smal...

Downloads & links

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Map

FileDownload / File: emd_1979.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSmall Hsp16.5 assembly
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.59 Å/pix.
x 128 pix.
= 203.52 Å		1.59 Å/pix.
x 128 pix.
= 203.52 Å		1.59 Å/pix.
x 128 pix.
= 203.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.59 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.0460981 - 0.0736925
Average (Standard dev.)0.0000429399 (±0.00846677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 203.52 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.591.591.59
M x/y/z128128128
origin x/y/z-0.000-0.000-0.000
length x/y/z203.520203.520203.520
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.0460.0740.000

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Supplemental data

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Sample components

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Entire : Hsp16.5 from Methanocaldococcus jannaschii

EntireName: Hsp16.5 from Methanocaldococcus jannaschii
Components
  • Sample: Hsp16.5 from Methanocaldococcus jannaschii
  • Protein or peptide: Small Heat Shock Protein

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Supramolecule #1000: Hsp16.5 from Methanocaldococcus jannaschii

SupramoleculeName: Hsp16.5 from Methanocaldococcus jannaschii / type: sample / ID: 1000 / Oligomeric state: 24mer / Number unique components: 1
Molecular weightTheoretical: 396 KDa

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Macromolecule #1: Small Heat Shock Protein

MacromoleculeName: Small Heat Shock Protein / type: protein_or_peptide / ID: 1 / Name.synonym: Small Heat Shock Protein / Oligomeric state: 24mer / Recombinant expression: Yes
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Molecular weightTheoretical: 396 KDa
SequenceGO: response to stress / InterPro: Alpha crystallin/Hsp20 domain

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7 / Details: 50 mM Tris
StainingType: NEGATIVE / Details: Staining with 1.5% (w/v) ammonium molybdate
GridDetails: 400 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 100CX
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 160,000 times magnification
DateMay 10, 2007
Image recordingCategory: FILM / Film or detector model: GENERIC CCD / Digitization - Scanner: OTHER / Digitization - Sampling interval: 7.9 µm / Bits/pixel: 16
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: JEOL

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Image processing

CTF correctionDetails: whole image
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC

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