7CK4

Structural and functional analysis of small heat shock protein from Synechococcus phage S-ShM2

• PDB DOI: https://doi.org/10.2210/pdb7CK4/pdb

• Classification: CHAPERONE
• Organism(s): Synechococcus phage S-ShM2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-07-15 Released: 2021-07-21 
• Deposition Author(s): Biswas, S., Suguna, K.
• Funding Organization(s): Department of Science & Technology (DST, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 7.00 Å
• R-Value Free: 0.433 
• R-Value Work: 0.346 
• R-Value Observed: 0.351 

Literature

Multiple nanocages of a cyanophage small heat shock protein with icosahedral and octahedral symmetries.

Biswas, S., Garg, P., Dutta, S., Suguna, K.

(2021) Sci Rep 11: 21023-21023

• PubMed: 34697325 
• DOI: https://doi.org/10.1038/s41598-021-00172-2
• Primary Citation of Related Structures:  
  7CK4


• PubMed Abstract: 
  

  The structures of a cyanophage small heat shock protein (sHSP) were determined as octahedrons of 24-mers and 48-mers and as icosahedrons of 60-mers. An N-terminal deletion construct of an 18 kDa sHSP of Synechococcus sp. phage S-ShM2 crystallized as a 24-mer and its structure was determined at a resolution of 7 Å. The negative stain electron microscopy (EM) images showed that the full-length protein is a mixture of a major population of larger and a minor population of smaller cage-like particles. Their structures have been determined by electron cryomicroscopy 3D image reconstruction at a resolution of 8 Å. The larger particles are 60-mers with icosahedral symmetry and the smaller ones are 48-mers with octahedral symmetry. These structures are the first of the viral/phage origin and the 60-mer is the largest and the first icosahedral assembly to be reported for sHSPs.

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Organizational Affiliation: 

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 116.96 kDa 
• Atom Count: 4,678 
• Modelled Residue Count: 598 
• Deposited Residue Count: 1,050 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein	A, B, C, D, E, F	175	Synechococcus phage S-ShM2	Mutation(s): 0  Gene Names: hsp20, SShM2_166
UniProt
Find proteins for E3SJI7 (Synechococcus phage S-ShM2) Explore E3SJI7  Go to UniProtKB:  E3SJI7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 7.00 Å
• R-Value Free: 0.433 
• R-Value Work: 0.346 
• R-Value Observed: 0.351 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.146	α = 90
b = 126.146	β = 90
c = 152.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Biswas, S., Suguna, K.

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Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	DST-1865

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2021-07-28
  Changes: Database references
• Version 1.2: 2021-08-04
  Changes: Derived calculations
• Version 1.3: 2022-02-09
  Changes: Database references
• Version 1.4: 2023-11-29
  Changes: Data collection, Refinement description