[English] 日本語
Yorodumi
- PDB-9ip0: Cryo-EM structure of ClpB1 heptamer from Oryza sativa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ip0
TitleCryo-EM structure of ClpB1 heptamer from Oryza sativa
ComponentsChaperone protein ClpB1
KeywordsPLANT PROTEIN / OsClpB
Function / homology
Function and homology information


cellular response to heat / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp, repeat (R) domain / Clp repeat (R) domain profile. / : ...ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp, repeat (R) domain / Clp repeat (R) domain profile. / : / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chaperone protein ClpB1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsJobichen, C. / Saharan, K. / Vasudevan, D. / Sivaraman, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Int J Biol Macromol / Year: 2025
Title: Cryo-EM structure provides insights into the unusual heptameric assembly of rice (Oryza sativa L.) ClpB1 AAA+ ATPase.
Authors: Chacko Jobichen / Ketul Saharan / Archana Samal / Yeu Khai Choong / Manas Kumar Jagdev / Chinmayee Mohapatra / Shi Jian / Richa Babbar / Renwick C J Dobson / Anil Grover / Dileep Vasudevan / J Sivaraman /
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 ...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.
History
DepositionJul 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperone protein ClpB1
B: Chaperone protein ClpB1
C: Chaperone protein ClpB1
D: Chaperone protein ClpB1
E: Chaperone protein ClpB1
F: Chaperone protein ClpB1
G: Chaperone protein ClpB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)713,30021
Polymers707,3197
Non-polymers5,98114
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Chaperone protein ClpB1 / ATP-dependent Clp protease ATP-binding subunit ClpB homolog 1 / Casein lytic proteinase B1 / Heat ...ATP-dependent Clp protease ATP-binding subunit ClpB homolog 1 / Casein lytic proteinase B1 / Heat shock protein 101


Mass: 101045.617 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: CLPB1, HSP101, Os05g0519700, LOC_Os05g44340, OsJ_19232, P0483D07.3, P0599F04.13
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6F2Y7
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Heptameric assembly of OsClpB1 protein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.700 MDa / Experimental value: NO
Source (natural)Organism: Oryza sativa (Asian cultivated rice)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170760 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00332487
ELECTRON MICROSCOPYf_angle_d0.71643932
ELECTRON MICROSCOPYf_dihedral_angle_d6.2024606
ELECTRON MICROSCOPYf_chiral_restr0.0445061
ELECTRON MICROSCOPYf_plane_restr0.0045705

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more