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- EMDB-1894: Cryo-EM structure of alphaB-crystallin 24mer -

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Basic information

Entry
Database: EMDB / ID: EMD-1894
TitleCryo-EM structure of alphaB-crystallin 24mer
Map dataVolume map of human alphaB-crystallin 24mer
Sample
  • Sample: Human alphaB crystallin
  • Protein or peptide: AlphaB crystallin
Keywordscryo electron microscopy / alphaB crystallin / molecular chaperone / protein aggregation / small heat shock protein / hybrid method
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 / M band / negative regulation of amyloid fibril formation / 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 / M band / negative regulation of amyloid fibril formation / 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 / negative regulation of cell growth / cellular response to gamma radiation / response to hydrogen peroxide / 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 / cryo EM / negative staining / Resolution: 9.4 Å
AuthorsBraun N / Zacharias M / Peschek J / Kastenmueller A / Hanzlik M / Haslbeck M / Buchner J / Weinkauf S
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Multiple molecular architectures of the eye lens chaperone αB-crystallin elucidated by a triple hybrid approach.
Authors: Nathalie Braun / Martin Zacharias / Jirka Peschek / Andreas Kastenmüller / Juan Zou / Marianne Hanzlik / Martin Haslbeck / Juri Rappsilber / Johannes Buchner / Sevil Weinkauf /
Abstract: The molecular chaperone αB-crystallin, the major player in maintaining the transparency of the eye lens, prevents stress-damaged and aging lens proteins from aggregation. In nonlenticular cells, it ...The molecular chaperone αB-crystallin, the major player in maintaining the transparency of the eye lens, prevents stress-damaged and aging lens proteins from aggregation. In nonlenticular cells, it is involved in various neurological diseases, diabetes, and cancer. Given its structural plasticity and dynamics, structure analysis of αB-crystallin presented hitherto a formidable challenge. Here we present a pseudoatomic model of a 24-meric αB-crystallin assembly obtained by a triple hybrid approach combining data from cryoelectron microscopy, NMR spectroscopy, and structural modeling. The model, confirmed by cross-linking and mass spectrometry, shows that the subunits interact within the oligomer in different, defined conformations. We further present the molecular architectures of additional well-defined αB-crystallin assemblies with larger or smaller numbers of subunits, provide the mechanism how "heterogeneity" is achieved by a small set of defined structural variations, and analyze the factors modulating the oligomer equilibrium of αB-crystallin and thus its chaperone activity.
History
DepositionApr 13, 2011-
Header (metadata) releaseApr 21, 2011-
Map releaseDec 1, 2011-
UpdateAug 29, 2012-
Current statusAug 29, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2ygd
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1894_1894.jpg

Downloads & links

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Map

FileDownload / File: emd_1894.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume map of human alphaB-crystallin 24mer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.8 Å/pix.
x 128 pix.
= 230.4 Å		1.8 Å/pix.
x 128 pix.
= 230.4 Å		1.8 Å/pix.
x 128 pix.
= 230.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum0.0 - 0.0804485
Average (Standard dev.)0.00482793 (±0.00703659)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 230.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z230.400230.400230.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean0.0000.0800.005

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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: Tetrahedral 24mer / Number unique components: 1
Molecular weightExperimental: 485 KDa / Theoretical: 485 KDa

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Macromolecule #1: AlphaB crystallin

MacromoleculeName: AlphaB crystallin / type: protein_or_peptide / ID: 1 / Name.synonym: Human alphaB crystallin / Number of copies: 24 / Oligomeric state: 24mer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 485 KDa
Recombinant expressionOrganism: Echerichia coli / Recombinant plasmid: pET28b
SequenceInterPro: INTERPRO: IPR012273

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4 / Details: PBS buffer
StainingType: NEGATIVE / Details: Vitrification
GridDetails: Quantifoil multi A (400 mesh copper grid)
VitrificationCryogen name: ETHANE / Chamber humidity: 50 % / Instrument: OTHER / Method: Blot for 1 second before plunging

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Electron microscopy

MicroscopeJEOL 2010HT
TemperatureAverage: 100 K
Image recordingDigitization - Scanner: OTHER / Digitization - Sampling interval: 8.47 µm / Number real images: 33 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 47000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each micrograph, phase flipping
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Number images used: 17560
Final two d classificationNumber classes: 878

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Atomic model buiding 1

Initial modelPDB ID:

2klr

DetailsPDB ID 2KLR was used for residues 69-150. Structure-elements for the remaining C- and N-termini were obtained by the found EM-Structure and structure prediction tools (fitted to the EM-Volume)
RefinementSpace: REAL
Output model

PDB-2ygd:
Molecular architectures of the 24meric eye lens chaperone alphaB- crystallin elucidated by a triple hybrid approach

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