5ZS6 | pdb_00005zs6

Dodecameric structure of a small Heat Shock Protein from Mycobacterium marinum M: Form-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.250 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5ZS6

This is version 1.2 of the entry. See complete history

Literature

Dodecameric structure of a small heat shock protein from Mycobacterium marinum M.

Bhandari, S.Biswas, S.Chaudhary, A.Dutta, S.Suguna, K.

(2019) Proteins 87: 365-379

  • DOI: https://doi.org/10.1002/prot.25657
  • Primary Citation Related Structures: 
    5ZS3, 5ZS6, 5ZUL

  • PubMed Abstract: 

    Small heat shock proteins (sHSPs) are ATP-independent molecular chaperones present ubiquitously in all kingdoms of life. Their low molecular weight subunits associate to form higher order structures. Under conditions of stress, sHSPs prevent aggregation of substrate proteins by undergoing rapid changes in their conformation or stoichiometry. Polydispersity and dynamic nature of these proteins have made structural investigations through crystallography a daunting task. In pathogens like Mycobacteria, sHSPs are immuno-dominant antigens, enabling survival of the pathogen within the host and contributing to disease persistence. We characterized sHSPs from Mycobacterium marinum M and determined the crystal structure of one of these. The protein crystallized in three different conditions as dodecamers, with dimers arranged in a tetrahedral fashion to form a closed cage-like architecture. Interestingly, we found a pentapeptide bound to the dodecamers revealing one of the modes of sHSP-substrate interaction. Further, we have observed that ATP inhibits the chaperoning activity of the protein.


  • Organizational Affiliation
    • Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Macromolecule Content 

  • Total Structure Weight: 17.52 kDa 
  • Atom Count: 902 
  • Modeled Residue Count: 116 
  • Deposited Residue Count: 153 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Molecular chaperone (Small heat shock protein)149Mycobacterium marinum MMutation(s): 0 
UniProt
Find proteins for B2HF11 (Mycobacterium marinum (strain ATCC BAA-535 / M))
Explore B2HF11 
Go to UniProtKB:  B2HF11
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2HF11
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GLY-ARG-LEU-LEUB [auth U]4Mycobacterium marinum MMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PRO

Query on PRO



Download:Ideal Coordinates CCD File
F [auth A]PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
I [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.250 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.29α = 90
b = 91.29β = 90
c = 91.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
India--

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description