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- EMDB-60751: Cryo-EM structure of ClpB1 heptamer from Oryza sativa -

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Basic information

Entry
Database: EMDB / ID: EMD-60751
TitleCryo-EM structure of ClpB1 heptamer from Oryza sativa
Map data
Sample
  • Complex: Heptameric assembly of OsClpB1 protein
    • Protein or peptide: Chaperone protein ClpB1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsOsClpB / PLANT PROTEIN
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
Chaperone protein ClpB1
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice) / Oryza sativa subsp. japonica (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsJobichen C / Saharan K / Vasudevan D / Sivaraman J
Funding support Singapore, 1 items
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, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60751.png

Downloads & links

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Map

FileDownload / File: emd_60751.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.106
Minimum - Maximum-0.4878884 - 0.8390789
Average (Standard dev.)0.0038153266 (±0.030553944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60751_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60751_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Heptameric assembly of OsClpB1 protein

EntireName: Heptameric assembly of OsClpB1 protein
Components
  • Complex: Heptameric assembly of OsClpB1 protein
    • Protein or peptide: Chaperone protein ClpB1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Heptameric assembly of OsClpB1 protein

SupramoleculeName: Heptameric assembly of OsClpB1 protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryza sativa (Asian cultivated rice)
Molecular weightTheoretical: 700 KDa

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Macromolecule #1: Chaperone protein ClpB1

MacromoleculeName: Chaperone protein ClpB1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Molecular weightTheoretical: 101.045617 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MNPDNFTHKT NEALVAAHEI ASEAGHAQLT PLHLVAALAA DKGGILRQAI SQASGGDAGA PDSFERVVSG ALKKLPSQSP PPDSVPAST ALIKVIRRAQ SAQKKRGDSH LAVDQLLLGL LEDSLISDCL KEAGVSAARV RAELEKLRGG EGRKVESASG D TNFQALKT ...String:
MNPDNFTHKT NEALVAAHEI ASEAGHAQLT PLHLVAALAA DKGGILRQAI SQASGGDAGA PDSFERVVSG ALKKLPSQSP PPDSVPAST ALIKVIRRAQ SAQKKRGDSH LAVDQLLLGL LEDSLISDCL KEAGVSAARV RAELEKLRGG EGRKVESASG D TNFQALKT YGRDLVEQAG KLDPVIGRDE EIRRVVRILS RRTKNNPVLI GEPGVGKTAV VEGLAQRIVR GDVPSNLLDV RL IALDMGA LVAGAKYRGE FEERLKAVLK EVEEAEGKVI LFIDEIHLVL GAGRTEGSMD AANLFKPMLA RGQLRCIGAT TLE EYRKYV EKDAAFERRF QQVFVAEPSV PDTISILRGL KEKYEGHHGV RIQDRALVVA AQLSARYIMG RHLPDKAIDL VDEA CANVR VQLDSQPEEI DNLERKRIQL EVEHHALEKE KDKASKARLV EVKKELDDLR DKLQPLTMKY RKEKERIDEI RKLKQ RREE LQFTLQEAER RMDLARVADL KYGALQEIDV AIAKLESETG ENLMLTETVG PEQIAEVVSR WTGIPVTRLG QNDKER LVG LADRLHQRVV GQAEAVSAVA EAVLRSRAGL GRPQQPTGSF LFLGPTGVGK TELAKALAEQ LFDDENLLVR IDMSEYM EQ HSVARLIGAP PGYVGHEEGG QLTEQVRRRP YSVILFDEVE KAHVAVFNTL LQVLDDGRLT DGQGRTVDFR NTVIIMTS N LGAEHLLAGM VGKNSMKVAR DLVMQEVRRH FRPELLNRLD EIVIFDPLSH EQLRKVARLQ MKDVAVRLAE RGVALAVTD AALDVILSLS YDPVYGARPI RRWIEKRVVT QLSKMLIQEE IDENCTVYID AAPHKDELAY RVDNRGGLVN AETGQKSDIL IQVPNGAAT GSDAAQAVKK MRIMEDEDGM DEE

UniProtKB: Chaperone protein ClpB1

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 14 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170760
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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