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- PDB-9nvc: mjHSP16.5 24mer (+lysozyme, 75C) -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9nvc
TitlemjHSP16.5 24mer (+lysozyme, 75C)
ComponentsSmall heat shock protein HSP16.5
KeywordsCHAPERONE / sHSP / thermophile / holdase
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 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsMiller, A.P. / Reichow, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI) United States
CitationJournal: Nat Commun / Year: 2025
Title: Mechanism of small heat shock protein client sequestration and induced polydispersity.
Authors: Adam P Miller / Steve L Reichow /
Abstract: Small heat shock proteins (sHSPs) act as first responders during cellular stress, sequestering destabilized proteins (clients) to prevent aggregation and facilitate refolding or degradation. This ...Small heat shock proteins (sHSPs) act as first responders during cellular stress, sequestering destabilized proteins (clients) to prevent aggregation and facilitate refolding or degradation. This critical function, conserved across all life, is linked to proteostasis and protein misfolding diseases. However, the extreme molecular plasticity of sHSP/client complexes has limited mechanistic understanding. Here, we present high-resolution cryo-EM structures of Methanocaldococcus jannaschii sHSP (mjHSP16.5) in apo and multiple client-bound states. The ensemble reveals molecular mechanisms of client sequestration, highlighting cooperative chaperone-client interactions. Client engagement polarizes scaffold stability, promoting higher-order assembly and enhanced sequestration. Higher-order states suggest multiple sHSP/client assembly pathways, including subunit insertion at destabilized geometrical features. These findings provide critical insights into sHSP chaperone function and the interplay between polydispersity and client handling under stress.
History
DepositionMar 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small heat shock protein HSP16.5
B: Small heat shock protein HSP16.5
D: Small heat shock protein HSP16.5
C: Small heat shock protein HSP16.5
E: Small heat shock protein HSP16.5
F: Small heat shock protein HSP16.5
G: Small heat shock protein HSP16.5
H: Small heat shock protein HSP16.5
I: Small heat shock protein HSP16.5
J: Small heat shock protein HSP16.5
K: Small heat shock protein HSP16.5
L: Small heat shock protein HSP16.5
M: Small heat shock protein HSP16.5
N: Small heat shock protein HSP16.5
O: Small heat shock protein HSP16.5
P: Small heat shock protein HSP16.5
Q: Small heat shock protein HSP16.5
R: Small heat shock protein HSP16.5
S: Small heat shock protein HSP16.5
T: Small heat shock protein HSP16.5
V: Small heat shock protein HSP16.5
W: Small heat shock protein HSP16.5
X: Small heat shock protein HSP16.5
Y: 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&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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 (archaea)
Gene: MJ0285 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57733
Has protein modificationN

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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: mjHSP16.5 24mer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 780906 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00422776
ELECTRON MICROSCOPYf_angle_d0.63830720
ELECTRON MICROSCOPYf_dihedral_angle_d12.8078880
ELECTRON MICROSCOPYf_chiral_restr0.0543672
ELECTRON MICROSCOPYf_plane_restr0.0033888

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