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- EMDB-80335: Cryo-EM structure of the E. coli beta sliding clamp-Hda heterohexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-80335
TitleCryo-EM structure of the E. coli beta sliding clamp-Hda heterohexamer
Map dataLocal-filtered 3DFlex refine map
Sample
  • Complex: Hetero-hexameric complex of beta sliding clamp and Hda
    • Protein or peptide: Beta sliding clamp
    • Protein or peptide: DnaA regulatory inactivator Hda
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsReplication inactivator / Inhibitor / ATPase / TRANSFERASE
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
Beta sliding clamp / DnaA regulatory inactivator Hda
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsJiang X / Danev R / Kikkawa M
Funding support Japan, 4 items
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, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_80335.png

Downloads & links

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Map

FileDownload / File: emd_80335.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal-filtered 3DFlex refine map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 192 pix.
= 219.264 Å		1.14 Å/pix.
x 192 pix.
= 219.264 Å		1.14 Å/pix.
x 192 pix.
= 219.264 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.142 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0035
Minimum - Maximum-0.07913557 - 0.105044276
Average (Standard dev.)0.00011609992 (±0.0014086877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 219.26399 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_80335_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3DFlex refine map

Fileemd_80335_additional_1.map
Annotation3DFlex refine map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local-filtered NU refine map

Fileemd_80335_additional_2.map
AnnotationLocal-filtered NU refine map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap2

Fileemd_80335_half_map_1.map
Annotationhalfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap1

Fileemd_80335_half_map_2.map
Annotationhalfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hetero-hexameric complex of beta sliding clamp and Hda

EntireName: Hetero-hexameric complex of beta sliding clamp and Hda
Components
  • Complex: Hetero-hexameric complex of beta sliding clamp and Hda
    • Protein or peptide: Beta sliding clamp
    • Protein or peptide: DnaA regulatory inactivator Hda
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Hetero-hexameric complex of beta sliding clamp and Hda

SupramoleculeName: Hetero-hexameric complex of beta sliding clamp and Hda
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 215 KDa

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Macromolecule #1: Beta sliding clamp

MacromoleculeName: Beta sliding clamp / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 42.801863 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MKFTVEREHL LKPLQQVSGP LGGRPTLPIL GNLLLQVADG TLSLTGTDLE MEMVARVALV QPHEPGATT VPARKFFDIC RGLPEGAEIA VQLEGERMLV RSGRSRFSLS TLPAADFPNL DDWQSEVEFT LPQATMKRLI E ATQFSMAH ...String:
MGSSHHHHHH SSGLVPRGSH MKFTVEREHL LKPLQQVSGP LGGRPTLPIL GNLLLQVADG TLSLTGTDLE MEMVARVALV QPHEPGATT VPARKFFDIC RGLPEGAEIA VQLEGERMLV RSGRSRFSLS TLPAADFPNL DDWQSEVEFT LPQATMKRLI E ATQFSMAH QDVRYYLNGM LFETEGEELR TVATDGHRLA VCSMPIGQSL PSHSVIVPRK GVIELMRMLD GGDNPLRVQI GS NNIRAHV GDFIFTSKLV DGRFPDYRRV LPKNPDKHLE AGCDLLKQAF ARAAILSNEK FRGVRLYVSE NQLKITANNP EQE EAEEIL DVTYSGAEME IGFNVSYVLD VLNALKCENV RMMLTDSVSS VQIEDAASQS AAYVVMPMRL

UniProtKB: Beta sliding clamp

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Macromolecule #2: DnaA regulatory inactivator Hda

MacromoleculeName: DnaA regulatory inactivator Hda / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.663678 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MNTPAQLSLP LYLPDDETFA SFWPGDNSSL LAALQNVLRQ EHSGYIYLWA REGAGRSHLL HAACAELSQR GDAVGYVPLD KRTWFVPEV LDGMEHLSLV CIDNIECIAG DELWEMAIFD LYNRILESGK TRLLITGDRP PRQLNLGLPD LASRLDWGQI Y KLQPLSDE ...String:
MNTPAQLSLP LYLPDDETFA SFWPGDNSSL LAALQNVLRQ EHSGYIYLWA REGAGRSHLL HAACAELSQR GDAVGYVPLD KRTWFVPEV LDGMEHLSLV CIDNIECIAG DELWEMAIFD LYNRILESGK TRLLITGDRP PRQLNLGLPD LASRLDWGQI Y KLQPLSDE DKLQALQLRA RLRGFELPED VGRFLLKRLD REMRTLFMTL DQLDRASITA QRKLTIPFVK EILKL

UniProtKB: DnaA regulatory inactivator Hda

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration1.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12396 / Average electron dose: 76.4 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.8 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.55 mm / Nominal defocus max: 1.3 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3682439
CTF correctionSoftware - Name: cryoSPARC (ver. 5.0.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-Initio Reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.0) / Number images used: 321931
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 5.0.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5x06


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: Docking of truncated 5X06 model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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