9IP0 | pdb_00009ip0

Cryo-EM structure of ClpB1 heptamer from Oryza sativa


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure provides insights into the unusual heptameric assembly of rice (Oryza sativa L.) ClpB1 AAA+ ATPase.

Jobichen, C.Saharan, K.Samal, A.Choong, Y.K.Jagdev, M.K.Mohapatra, C.Jian, S.Babbar, R.Dobson, R.C.J.Grover, A.Vasudevan, D.Sivaraman, J.

(2025) Int J Biol Macromol 311: 143917-143917

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.143917
  • Primary Citation of Related Structures:  
    9IP0

  • PubMed Abstract: 

    Heat stress disrupts the protein homeostasis leading to the accumulation of toxic aggregated proteins in the cell. ClpB disaggregase belonging to the AAA+ ATPase superfamily removes the aggregated toxic proteins. ClpB is present ubiquitously in bacteria, yeast, protozoans and plants and plays a role in acquired heat tolerance. This study was focused on cytoplasmic ClpB1 from rice which is the staple food for more than half of world's population. In bacteria and yeast, ClpB forms a hexameric assembly for carrying out the disaggregase function, however, none of the plant ClpB isoforms have been structurally characterized. Here, we report the cryo-EM structure of ClpB1 from rice (Oryza sativa L.; OsClpB1) at 4 Å resolution. The structure reveals that OsClpB1 assembles as an unusual heptameric ring, possibly representing a non-processive open conformation. Our results point to the structural plasticity of OsClpB1 since it exists in different oligomeric forms. Analytical ultracentrifugation studies confirmed OsClpB1 exist as a heptamer in solution as well, suggesting the presence of the heptameric form of OsClpB1 within the cellular milieu of the rice plant.


  • Organizational Affiliation
    • School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore. Electronic address: J.Chacko@uq.edu.au.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperone protein ClpB1
A, B, C, D, E
A, B, C, D, E, F, G
912Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: CLPB1HSP101Os05g0519700LOC_Os05g44340OsJ_19232P0483D07.3P0599F04.13
UniProt
Find proteins for Q6F2Y7 (Oryza sativa subsp. japonica)
Explore Q6F2Y7 
Go to UniProtKB:  Q6F2Y7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6F2Y7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth B]
K [auth B]
L [auth C]
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth C],
M [auth C],
N [auth D],
O [auth D],
P [auth E],
Q [auth E],
R [auth F],
S [auth F],
T [auth G],
U [auth G]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Data collection, Database references
  • Version 1.2: 2025-06-18
    Changes: Data collection