8WP9 | pdb_00008wp9

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8WP9

This is version 1.0 of the entry. See complete history

Literature

Cryo-EM structure of a 16.5-kDa small heat-shock protein from Methanocaldococcus jannaschii.

Lee, J.Ryu, B.Kim, T.Kim, K.K.

(2024) Int J Biol Macromol 258: 128763-128774

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.128763
  • Primary Citation Related Structures: 
    8WP9

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 395.28 kDa 
  • Atom Count: 21,432 
  • Modeled Residue Count: 2,760 
  • Deposited Residue Count: 3,528 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Small heat shock protein HSP16.5147Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: MJ0285
UniProt
Find proteins for Q57733 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57733 
Go to UniProtKB:  Q57733
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57733
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.4.6
MODEL REFINEMENTcryoSPARC2.4.6

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2021M3A914022936
National Research Foundation (NRF, Korea)Korea, Republic Of2017R1D1A1B03031067
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2023-00217189

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release