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- EMDB-1776: The eye lens chaperone alphaB-crystallin forms defined globular, ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1776 | |||||||||
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Title | The eye lens chaperone alphaB-crystallin forms defined globular, 24meric assemblies | |||||||||
![]() | This is a map of human alphaB crystallin | |||||||||
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![]() | Molecular chaperone / Protein Aggregation / Small Heat Shock Protein / Stress Response | |||||||||
Function / homology | ![]() 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 / muscle contraction / stress-activated MAPK cascade / 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 / protein refolding / response to heat / microtubule binding / perikaryon / dendritic spine / lysosome / response to hypoxia / protein stabilization / axon / negative regulation of gene expression / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / protein-containing complex binding / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||
![]() | Peschek J / Braun N / Franzmann TM / Georgalis Y / Haslbeck M / Weinkauf S / Buchner J | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 11.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.8 KB 9.8 KB | Display Display | ![]() |
Images | ![]() ![]() | 61.2 KB 100.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 208.7 KB | Display | ![]() |
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Full document | ![]() | 207.8 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3j07M M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | This is a map of human alphaB crystallin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.69 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Human alphaB crystallin
Entire | Name: Human alphaB crystallin |
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Components |
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-Supramolecule #1000: Human alphaB crystallin
Supramolecule | Name: Human alphaB crystallin / type: sample / ID: 1000 / Oligomeric state: 24-mer / Number unique components: 1 |
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Molecular weight | Theoretical: 485 KDa |
-Macromolecule #1: alphaB crystallin
Macromolecule | Name: alphaB crystallin / type: protein_or_peptide / ID: 1 / Name.synonym: Small heat shock protein / Number of copies: 24 / Oligomeric state: 24mer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 7.4 / Details: 137mM NaCl, 2.7mM KCl, 12 mM PBS |
Staining | Type: NEGATIVE Details: Samples were negatively stained for 30s using Ammonium Molybdate solution pH 5.5 |
Grid | Details: 300 mesh carbon-coated copper grids |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | JEOL 100CX |
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Date | Feb 6, 2008 |
Image recording | Category: 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 beam | Acceleration voltage: 100 kV / Electron source: OTHER |
Electron optics | Illumination 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 stage | Specimen holder: Side entry / Specimen holder model: JEOL |
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Image processing
Details | After 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 |
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CTF correction | Details: Phase flipping of each particle |
Final reconstruction | Applied 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 classification | Number classes: 40 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: C |
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Software | Name: ![]() |
Details | PDBEntryID_givenInChain. The dimers were separately fitted by manual docking using program chimera. AS 14-103 were used |
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-3j07: |