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- PDB-8wp9: Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5 -

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Basic information

Entry
Database: PDB / ID: 8wp9
TitleSmall-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5
ComponentsSmall heat shock protein HSP16.5
KeywordsCHAPERONE / Hsp16.5 / molecular chaperone / oligomeric protein / small heat-shock protein / stress response
Function / homology
Function and homology information


protein complex oligomerization / response to salt stress / protein folding chaperone / response to hydrogen peroxide / unfolded protein binding / protein folding / response to heat / protein stabilization / protein-containing complex / identical protein binding / 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
Small heat shock protein HSP16.5
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsLee, J. / Ryu, B. / Kim, T. / Kim, K.K.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021M3A914022936 Korea, Republic Of
National Research Foundation (NRF, Korea)2017R1D1A1B03031067 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2023-00217189 Korea, Republic Of
CitationJournal: Int J Biol Macromol / Year: 2024
Title: Cryo-EM structure of a 16.5-kDa small heat-shock protein from Methanocaldococcus jannaschii.
Authors: Joohyun Lee / Bumhan Ryu / Truc Kim / Kyeong Kyu Kim /
Abstract: The small heat-shock protein (sHSP) from the archaea Methanocaldococcus jannaschii, MjsHSP16.5, functions as a broad substrate ATP-independent holding chaperone protecting misfolded proteins from ...The small heat-shock protein (sHSP) from the archaea Methanocaldococcus jannaschii, MjsHSP16.5, functions as a broad substrate ATP-independent holding chaperone protecting misfolded proteins from aggregation under stress conditions. This protein is the first sHSP characterized by X-ray crystallography, thereby contributing significantly to our understanding of sHSPs. However, despite numerous studies assessing its functions and structures, the precise arrangement of the N-terminal domains (NTDs) within this sHSP cage remains elusive. Here we present the cryo-electron microscopy (cryo-EM) structure of MjsHSP16.5 at 2.49-Å resolution. The subunits of MjsHSP16.5 in the cryo-EM structure exhibit lesser compaction compared to their counterparts in the crystal structure. This structural feature holds particular significance in relation to the biophysical properties of MjsHSP16.5, suggesting a close resemblance to this sHSP native state. Additionally, our cryo-EM structure unveils the density of residues 24-33 within the NTD of MjsHSP16.5, a feature that typically remains invisible in the majority of its crystal structures. Notably, these residues show a propensity to adopt a β-strand conformation and engage in antiparallel interactions with strand β1, both intra- and inter-subunit modes. These structural insights are corroborated by structural predictions, disulfide bond cross-linking studies of Cys-substitution mutants, and protein disaggregation assays. A comprehensive understanding of the structural features of MjsHSP16.5 expectedly holds the potential to inspire a wide range of interdisciplinary applications, owing to the renowned versatility of this sHSP as a nanoscale protein platform.
History
DepositionOct 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small heat shock protein HSP16.5
P: Small heat shock protein HSP16.5
T: Small heat shock protein HSP16.5
U: Small heat shock protein HSP16.5
E: Small heat shock protein HSP16.5
I: Small heat shock protein HSP16.5
X: Small heat shock protein HSP16.5
D: Small heat shock protein HSP16.5
F: Small heat shock protein HSP16.5
R: Small heat shock protein HSP16.5
O: Small heat shock protein HSP16.5
C: Small heat shock protein HSP16.5
B: Small heat shock protein HSP16.5
W: Small heat shock protein HSP16.5
K: Small heat shock protein HSP16.5
N: Small heat shock protein HSP16.5
H: Small heat shock protein HSP16.5
L: Small heat shock protein HSP16.5
M: Small heat shock protein HSP16.5
Q: Small heat shock protein HSP16.5
J: Small heat shock protein HSP16.5
G: Small heat shock protein HSP16.5
S: Small heat shock protein HSP16.5
V: Small heat shock protein HSP16.5


Theoretical massNumber of molelcules
Total (without water)395,28024
Polymers395,28024
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Small heat shock protein HSP16.5


Mass: 16469.990 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: MJ0285 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57733

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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 from Methanocaldococcus jannaschii, Hsp16.5
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.396 MDa / Experimental value: NO
Source (natural)Organism: Methanocaldococcus jannaschii DSM 2661 (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
SpecimenConc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC2.4.6particle selection
4CTFFIND4CTF correction
9cryoSPARC2.4.6initial Euler assignment
10cryoSPARC2.4.6final Euler assignment
12cryoSPARC2.4.63D reconstruction
13cryoSPARC2.4.6model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 242099
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205569 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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