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- EMDB-37713: Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5 -

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Basic information

Entry
Database: EMDB / ID: EMD-37713
TitleSmall-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5
Map data
Sample
  • Complex: Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5
    • Protein or peptide: Small heat shock protein HSP16.5
KeywordsHsp16.5 / molecular chaperone / oligomeric protein / small heat-shock protein / stress response / CHAPERONE
Function / homology
Function and homology information


protein folding chaperone / response to salt stress / response to hydrogen peroxide / : / unfolded protein binding / protein folding / protein complex oligomerization / response to heat / protein stabilization / protein-containing complex ...protein folding chaperone / response to salt stress / response to hydrogen peroxide / : / unfolded protein binding / protein folding / protein complex oligomerization / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsLee J / Ryu B / Kim T / Kim KK
Funding support Korea, Republic Of, 3 items
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, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37713.png

Downloads & links

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Map

FileDownload / File: emd_37713.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.673 Å
Density
Contour LevelBy AUTHOR: 0.723
Minimum - Maximum-2.5506134 - 3.9405267
Average (Standard dev.)0.0009076415 (±0.15463279)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 258.432 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37713_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: #1

Fileemd_37713_additional_1.map
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Half map: #1

Fileemd_37713_half_map_1.map
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Half map: #2

Fileemd_37713_half_map_2.map
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Sample components

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Entire : Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5

EntireName: Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5
Components
  • Complex: Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5
    • Protein or peptide: Small heat shock protein HSP16.5

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Supramolecule #1: Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5

SupramoleculeName: Small-heat shock protein from Methanocaldococcus jannaschii, Hsp16.5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Methanocaldococcus jannaschii DSM 2661 (archaea)
Molecular weightTheoretical: 396 KDa

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Macromolecule #1: Small heat shock protein HSP16.5

MacromoleculeName: Small heat shock protein HSP16.5 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Methanocaldococcus jannaschii DSM 2661 (archaea)
Molecular weightTheoretical: 16.46999 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MFGRDPFDSL FERMFKEFFA TPMTGTTMIQ SSTGIQISGK GFMPISIIEG DQHIKVIAWL PGVNKEDIIL NAVGDTLEIR AKRSPLMIT ESERIIYSEI PEEEEIYRTI KLPATVKEEN ASAKFENGVL SVILPKAESS IKKGINIE

UniProtKB: Small heat shock protein HSP16.5

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.7 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 242099
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.4.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.4.6)
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.4.6) / Number images used: 205569
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

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

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