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- PDB-2h53: Multiple distinct assemblies reveal conformational flexibility in... -

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Basic information

Entry
Database: PDB / ID: 2h53
TitleMultiple distinct assemblies reveal conformational flexibility in the small heat shock protein Hsp26
Componentssmall heat shock protein Hsp26
KeywordsCHAPERONE / alpha-crystallin / chaperones / heat shock proteins / single particle reconstruction
Function / homology
Function and homology information


response to salt stress / response to hydrogen peroxide / protein homooligomerization / protein self-association / unfolded protein binding / protein complex oligomerization / protein folding / response to heat / cytoplasm
Similarity search - Function
: / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone
Similarity search - Domain/homology
16.9 kDa class I heat shock protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsWhite, H.E. / Orlova, E.V. / Chen, S. / Wang, L. / Ignatiou, A. / Gowen, B. / Stromer, T. / Franzmann, T.M. / Haslbeck, M. / Buchner, J. / Saibil, H.R.
CitationJournal: Structure / Year: 2006
Title: Multiple distinct assemblies reveal conformational flexibility in the small heat shock protein Hsp26.
Authors: Helen E White / Elena V Orlova / Shaoxia Chen / Luchun Wang / Athanasios Ignatiou / Brent Gowen / Thusnelda Stromer / Titus M Franzmann / Martin Haslbeck / Johannes Buchner / Helen R Saibil /
Abstract: Small heat shock proteins are a superfamily of molecular chaperones that suppress protein aggregation and provide protection from cell stress. A key issue for understanding their action is to define ...Small heat shock proteins are a superfamily of molecular chaperones that suppress protein aggregation and provide protection from cell stress. A key issue for understanding their action is to define the interactions of subunit domains in these oligomeric assemblies. Cryo-electron microscopy of yeast Hsp26 reveals two distinct forms, each comprising 24 subunits arranged in a porous shell with tetrahedral symmetry. The subunits form elongated, asymmetric dimers that assemble via trimeric contacts. Modifications of both termini cause rearrangements that yield a further four assemblies. Each subunit contains an N-terminal region, a globular middle domain, the alpha-crystallin domain, and a C-terminal tail. Twelve of the C termini form 3-fold assembly contacts which are inserted into the interior of the shell, while the other 12 C termini form contacts on the surface. Hinge points between the domains allow a variety of assembly contacts, providing the flexibility required for formation of supercomplexes with non-native proteins.
History
DepositionMay 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 15, 2014Group: Database references
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.5Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.6Feb 14, 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 999SEQUENCE THE SEQUENCE LISTED HERE IS THAT OF HEAT SHOCK PROTEIN 16.9B CORRESPONDING TO THE PDB ...SEQUENCE THE SEQUENCE LISTED HERE IS THAT OF HEAT SHOCK PROTEIN 16.9B CORRESPONDING TO THE PDB ENTRY 1GME. THE ACTUAL SEQUENCE IN THE SAMPLE IS THAT OF UNIPROT ENTRY P15992.

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Structure visualization

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Assembly

Deposited unit
A: small heat shock protein Hsp26
B: small heat shock protein Hsp26
C: small heat shock protein Hsp26
D: small heat shock protein Hsp26
E: small heat shock protein Hsp26
F: small heat shock protein Hsp26
G: small heat shock protein Hsp26
H: small heat shock protein Hsp26
I: small heat shock protein Hsp26
J: small heat shock protein Hsp26
K: small heat shock protein Hsp26
L: small heat shock protein Hsp26
M: small heat shock protein Hsp26
N: small heat shock protein Hsp26
O: small heat shock protein Hsp26
P: small heat shock protein Hsp26
Q: small heat shock protein Hsp26
R: small heat shock protein Hsp26
S: small heat shock protein Hsp26
T: small heat shock protein Hsp26
U: small heat shock protein Hsp26
V: small heat shock protein Hsp26
W: small heat shock protein Hsp26
X: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)256,32424
Polymers256,32424
Non-polymers00
Water0
1
M: small heat shock protein Hsp26
N: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)21,3602
Polymers21,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-6 kcal/mol
Surface area11400 Å2
MethodPISA, PQS
2
O: small heat shock protein Hsp26
P: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)21,3602
Polymers21,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-6 kcal/mol
Surface area11400 Å2
MethodPISA, PQS
3
S: small heat shock protein Hsp26
T: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)21,3602
Polymers21,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-6 kcal/mol
Surface area11420 Å2
MethodPISA, PQS
4
W: small heat shock protein Hsp26
X: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)21,3602
Polymers21,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-6 kcal/mol
Surface area11420 Å2
MethodPISA, PQS
5
K: small heat shock protein Hsp26
L: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)21,3602
Polymers21,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-6 kcal/mol
Surface area11390 Å2
MethodPISA, PQS
6
I: small heat shock protein Hsp26
J: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)21,3602
Polymers21,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-6 kcal/mol
Surface area11390 Å2
MethodPISA, PQS
7
E: small heat shock protein Hsp26
F: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)21,3602
Polymers21,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-5 kcal/mol
Surface area11420 Å2
MethodPISA, PQS
8
C: small heat shock protein Hsp26
D: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)21,3602
Polymers21,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-5 kcal/mol
Surface area11420 Å2
MethodPISA, PQS
9
A: small heat shock protein Hsp26
B: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)21,3602
Polymers21,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-5 kcal/mol
Surface area11420 Å2
MethodPISA, PQS
10
G: small heat shock protein Hsp26
H: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)21,3602
Polymers21,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-5 kcal/mol
Surface area11420 Å2
MethodPISA, PQS
11
Q: small heat shock protein Hsp26
R: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)21,3602
Polymers21,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-5 kcal/mol
Surface area11410 Å2
MethodPISA, PQS
12
U: small heat shock protein Hsp26
V: small heat shock protein Hsp26


Theoretical massNumber of molelcules
Total (without water)21,3602
Polymers21,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-5 kcal/mol
Surface area11410 Å2
MethodPISA, PQS

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Components

#1: Protein ...
small heat shock protein Hsp26


Mass: 10680.172 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q41560*PLUS
Sequence detailsEXPERIMENTAL SAMPLE SEQUENCE COME FROM YEAST. MODEL SEQUENCE COME FROM WHEAT.

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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: small heat shock protein Hsp26 complex / Type: COMPLEX
Buffer solutionName: 40 mM Hepes, 50 mM NaCl, 2 mM EDTA, 1 mM DTT / pH: 7.4 / Details: 40 mM Hepes, 50 mM NaCl, 2 mM EDTA, 1 mM DTT
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 38000 X / Nominal defocus max: 3400 nm / Nominal defocus min: 1700 nm
Image recordingFilm or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UROmodel fitting
2IMAGIC3D reconstruction
CTF correctionDetails: Phase flipping
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionMethod: ANGULAR RECONSTITUTION / Resolution: 11.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 5000 / Nominal pixel size: 1.86 Å / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: best visual fit using the program O / Details: REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 1GME
Accession code: 1GME / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms18000 0 0 0 18000

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