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- PDB-25rz: Cryo-EM structure of the E. coli beta sliding clamp-Hda heterohexamer -

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Basic information

Entry
Database: PDB / ID: 25rz
TitleCryo-EM structure of the E. coli beta sliding clamp-Hda heterohexamer
Components
  • Beta sliding clamp
  • DnaA regulatory inactivator Hda
KeywordsTRANSFERASE / Replication inactivator / Inhibitor / ATPase
Function / homology
Function and homology information


replication inhibiting complex / Hda-beta clamp complex / DNA polymerase III complex / DNA strand elongation involved in DNA replication / DNA replication initiation / regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / negative regulation of DNA-templated DNA replication initiation / ADP binding / DNA replication ...replication inhibiting complex / Hda-beta clamp complex / DNA polymerase III complex / DNA strand elongation involved in DNA replication / DNA replication initiation / regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / negative regulation of DNA-templated DNA replication initiation / ADP binding / DNA replication / DNA-directed DNA polymerase activity / DNA binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DnaA regulatory inactivator Hda, Enterobacteriaceae / : / DnaA regulatory inactivator Hda / Hda, lid domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal ...DnaA regulatory inactivator Hda, Enterobacteriaceae / : / DnaA regulatory inactivator Hda / Hda, lid domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / : / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Beta sliding clamp / DnaA regulatory inactivator Hda
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsJiang, X. / Danev, R. / Kikkawa, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJER2202 Japan
Japan Society for the Promotion of Science (JSPS)JP21H05247 Japan
Japan Society for the Promotion of Science (JSPS)JP24KF0141 Japan
Japan Society for the Promotion of Science (JSPS)JP24K18106 Japan
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Reversible autoinhibition of the bacterial replication-licensing Hda-beta clamp complex.
Authors: Jiang, X. / Danev, R. / Luan, Y. / Nakakido, M. / Tsumoto, K. / Kikkawa, M.
History
DepositionApr 16, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta sliding clamp
B: Beta sliding clamp
C: Beta sliding clamp
D: Beta sliding clamp
E: DnaA regulatory inactivator Hda
F: DnaA regulatory inactivator Hda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,43810
Polymers224,5356
Non-polymers9034
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Beta sliding clamp / Beta clamp / Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp ...Beta clamp / Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp subunit / DNA polymerase III subunit beta


Mass: 42801.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaN, Z5192, ECs4636 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A990
#2: Protein DnaA regulatory inactivator Hda / DnaA paralog / Dp / Protein IdaB


Mass: 26663.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hda, idaB, yfgE, b2496, JW5397, f248c / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P69931
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Hetero-hexameric complex of beta sliding clamp and Hda
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.215 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 / Plasmid: pETDuet-1 for KIF3A/B, pET21b for KAP3
Buffer solutionpH: 7.5
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 80000 X / Nominal defocus max: 1300 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 1800 nm / Cs: 1.55 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 76.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12396
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC5.0.0particle selection
2SerialEMimage acquisition
4cryoSPARC5.0.0CTF correction
7PHENIXmodel fitting
9cryoSPARC5.0.0initial Euler assignment
10cryoSPARC5.0.0final Euler assignment
11cryoSPARC5.0.0classification
12cryoSPARC5.0.03D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3682439
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 321931 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 5X06

5x06


Accession code: 5X06 / Details: Docking of truncated 5X06 model / Source name: PDB / Type: experimental model

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