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- EMDB-1776: The eye lens chaperone alphaB-crystallin forms defined globular, ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1776
TitleThe eye lens chaperone alphaB-crystallin forms defined globular, 24meric assemblies
Map dataThis is a map of human alphaB crystallin
Sample
  • Sample: Human alphaB crystallin
  • Protein or peptide: alphaB crystallin
KeywordsMolecular chaperone / Protein Aggregation / Small Heat Shock Protein / Stress Response
Function / homology
Function and homology information


microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / cardiac myofibril / regulation of programmed cell death / tubulin complex assembly / structural constituent of eye lens / negative regulation of amyloid fibril formation / M band / lens development in camera-type eye ...microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / cardiac myofibril / regulation of programmed cell death / tubulin complex assembly / structural constituent of eye lens / negative regulation of amyloid fibril formation / M band / lens development in camera-type eye / muscle organ development / actin filament bundle / HSF1-dependent transactivation / negative regulation of reactive oxygen species metabolic process / negative regulation of protein-containing complex assembly / stress-activated MAPK cascade / muscle contraction / synaptic membrane / response to hydrogen peroxide / negative regulation of cell growth / cellular response to gamma radiation / Z disc / unfolded protein binding / protein folding / response to estradiol / amyloid-beta binding / response to heat / protein refolding / microtubule binding / perikaryon / dendritic spine / lysosome / response to hypoxia / protein stabilization / axon / negative regulation of gene expression / negative regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of apoptotic process / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Alpha-crystallin B chain, ACD domain / Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone
Similarity search - Domain/homology
Alpha-crystallin B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsPeschek J / Braun N / Franzmann TM / Georgalis Y / Haslbeck M / Weinkauf S / Buchner J
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: The eye lens chaperone alpha-crystallin forms defined globular assemblies.
Authors: Jirka Peschek / Nathalie Braun / Titus M Franzmann / Yannis Georgalis / Martin Haslbeck / Sevil Weinkauf / Johannes Buchner /
Abstract: Alpha-crystallins are molecular chaperones that protect vertebrate eye lens proteins from detrimental protein aggregation. alphaB-Crystallin, 1 of the 2 alpha-crystallin isoforms, is also associated ...Alpha-crystallins are molecular chaperones that protect vertebrate eye lens proteins from detrimental protein aggregation. alphaB-Crystallin, 1 of the 2 alpha-crystallin isoforms, is also associated with myopathies and neuropathological diseases. Despite the importance of alpha-crystallins in protein homeostasis, only little is known about their quaternary structures because of their seemingly polydisperse nature. Here, we analyzed the structures of recombinant alpha-crystallins using biophysical methods. In contrast to previous reports, we show that alphaB-crystallin assembles into defined oligomers consisting of 24 subunits. The 3-dimensional (3D) reconstruction of alphaB-crystallin by electron microscopy reveals a sphere-like structure with large openings to the interior of the protein. alphaA-Crystallin forms, in addition to complexes of 24 subunits, also smaller oligomers and large clusters consisting of individual oligomers. This propensity might explain the previously reported polydisperse nature of alpha-crystallin.
History
DepositionAug 31, 2010-
Header (metadata) releaseSep 10, 2010-
Map releaseSep 10, 2010-
UpdateSep 19, 2012-
Current statusSep 19, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.081
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.081
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j07
  • Surface level: 0.081
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1776.gif

EMD-1776.jpg

Downloads & links

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Map

FileDownload / File: emd_1776.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of human alphaB crystallin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 150 pix.
= 253.5 Å		1.69 Å/pix.
x 150 pix.
= 253.5 Å		1.69 Å/pix.
x 150 pix.
= 253.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.081 / Movie #1: 0.081
Minimum - Maximum-0.09503739 - 0.28221357
Average (Standard dev.)-0.00120769 (±0.03652364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 253.50002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.691.691.69
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z253.500253.500253.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.0950.282-0.001

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Supplemental data

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Sample components

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Entire : Human alphaB crystallin

EntireName: Human alphaB crystallin
Components
  • Sample: Human alphaB crystallin
  • Protein or peptide: alphaB crystallin

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Supramolecule #1000: Human alphaB crystallin

SupramoleculeName: Human alphaB crystallin / type: sample / ID: 1000 / Oligomeric state: 24-mer / Number unique components: 1
Molecular weightTheoretical: 485 KDa

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Macromolecule #1: alphaB crystallin

MacromoleculeName: alphaB crystallin / type: protein_or_peptide / ID: 1 / Name.synonym: Small heat shock protein / Number of copies: 24 / Oligomeric state: 24mer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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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

Concentration0.05 mg/mL
BufferpH: 7.4 / Details: 137mM NaCl, 2.7mM KCl, 12 mM PBS
StainingType: NEGATIVE
Details: Samples were negatively stained for 30s using Ammonium Molybdate solution pH 5.5
GridDetails: 300 mesh carbon-coated copper grids
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 100CX
DateFeb 6, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 1.69 µm / Number real images: 11 / Bits/pixel: 16
Electron beamAcceleration voltage: 100 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.8 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry / Specimen holder model: JEOL

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Image processing

DetailsAfter correction of contrast transfer function by phase flipping the reconstructions have been performed by iterative cycles of MRA, MSA, classification and angular reconstitution of the obtained class averages. See also publication Peschek et al., 2009. The eye lens chaperone alpha-crystallin forms defined globular assemblies. PNAS 106
CTF correctionDetails: Phase flipping of each particle
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Details: Final maps were calculated from 40 class averages / Number images used: 2565
Final two d classificationNumber classes: 40

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Atomic model buiding 1

Initial modelPDB ID:

1shs


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: C
SoftwareName: Chimera
DetailsPDBEntryID_givenInChain. The dimers were separately fitted by manual docking using program chimera. AS 14-103 were used
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-3j07:
Model of a 24mer alphaB-crystallin multimer

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