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- PDB-2ygd: Molecular architectures of the 24meric eye lens chaperone alphaB-... -

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Entry
Database: PDB / ID: 2ygd
TitleMolecular architectures of the 24meric eye lens chaperone alphaB- crystallin elucidated by a triple hybrid approach
ComponentsALPHA-CRYSTALLIN B CHAIN
KeywordsCHAPERONE / PROTEIN AGGREGATION / HYBRID METHOD
Function / homology
Function and homology information


microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / regulation of programmed cell death / cardiac myofibril / 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 / regulation of programmed cell death / cardiac myofibril / 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 / negative regulation of reactive oxygen species metabolic process / HSF1-dependent transactivation / negative regulation of protein-containing complex assembly / stress-activated MAPK cascade / muscle contraction / synaptic membrane / response to hydrogen peroxide / cellular response to gamma radiation / negative regulation of cell growth / Z disc / unfolded protein binding / response to estradiol / protein folding / amyloid-beta binding / response to heat / protein refolding / perikaryon / microtubule binding / dendritic spine / response to hypoxia / lysosome / protein stabilization / negative regulation of gene expression / axon / 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 / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.4 Å
AuthorsBraun, N. / Zacharias, M. / Peschek, J. / Kastenmueller, A. / Zou, J. / Hanzlik, M. / Haslbeck, M. / Rappsilber, J. / 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, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Other
Revision 1.2Nov 20, 2013Group: Source and taxonomy
Revision 1.3Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id
Revision 1.4May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "MC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "SC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Assembly

Deposited unit
A: ALPHA-CRYSTALLIN B CHAIN
B: ALPHA-CRYSTALLIN B CHAIN
C: ALPHA-CRYSTALLIN B CHAIN
D: ALPHA-CRYSTALLIN B CHAIN
E: ALPHA-CRYSTALLIN B CHAIN
F: ALPHA-CRYSTALLIN B CHAIN
G: ALPHA-CRYSTALLIN B CHAIN
H: ALPHA-CRYSTALLIN B CHAIN
I: ALPHA-CRYSTALLIN B CHAIN
J: ALPHA-CRYSTALLIN B CHAIN
K: ALPHA-CRYSTALLIN B CHAIN
L: ALPHA-CRYSTALLIN B CHAIN
M: ALPHA-CRYSTALLIN B CHAIN
N: ALPHA-CRYSTALLIN B CHAIN
O: ALPHA-CRYSTALLIN B CHAIN
P: ALPHA-CRYSTALLIN B CHAIN
Q: ALPHA-CRYSTALLIN B CHAIN
R: ALPHA-CRYSTALLIN B CHAIN
S: ALPHA-CRYSTALLIN B CHAIN
T: ALPHA-CRYSTALLIN B CHAIN
U: ALPHA-CRYSTALLIN B CHAIN
V: ALPHA-CRYSTALLIN B CHAIN
W: ALPHA-CRYSTALLIN B CHAIN
X: ALPHA-CRYSTALLIN B CHAIN


Theoretical massNumber of molelcules
Total (without water)484,60624
Polymers484,60624
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
ALPHA-CRYSTALLIN B CHAIN / ALPHAB CRYSTALLIN / ALPHA(B)-CRYSTALLIN / HEAT SHOCK PROTEIN BETA-5 / HSPB5 / RENAL CARCINOMA ...ALPHAB CRYSTALLIN / ALPHA(B)-CRYSTALLIN / HEAT SHOCK PROTEIN BETA-5 / HSPB5 / RENAL CARCINOMA ANTIGEN NY-REN-27 / ROSENTHAL FIBER COMPONENT


Mass: 20191.930 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02511

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HUMAN ALPHAB CRYSTALLIN / Type: COMPLEX
Buffer solutionName: PBS BUFFER / pH: 7.4 / Details: PBS BUFFER
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 50, METHOD- BLOT FOR 1 SECOND BEFORE PLUNGING,

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Electron microscopy imaging

MicroscopyModel: JEOL 2010HT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 47000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 10 e/Å2
Image scansNum. digital images: 33

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Processing

EM softwareName: IMAGIC / Category: 3D reconstruction
CTF correctionDetails: EACH MICROGRAPH, PHASE FLIPPING
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 9.4 Å / Num. of particles: 17560 / Nominal pixel size: 1.69 Å / Actual pixel size: 1.8 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA EMDB EMD-1894.(DEPOSITION ID: 7925).
Symmetry type: POINT
Atomic model buildingPDB-ID: 2KLR

2klr


Accession code: 2KLR / Source name: PDB / Type: experimental model
RefinementHighest resolution: 9.4 Å
Refinement stepCycle: LAST / Highest resolution: 9.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34296 0 0 0 34296

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