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- EMDB-80433: Cryo-EM structure of the E. coli beta sliding clamp -

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Basic information

Entry
Database: EMDB / ID: EMD-80433
TitleCryo-EM structure of the E. coli beta sliding clamp
Map datasharpened map
Sample
  • Complex: E. coli beta sliding clamp
    • Protein or peptide: Beta sliding clamp
KeywordsDNA clamp / Sliding clamp / DNA polymerase III subunit / Processivity-promoting factor / REPLICATION
Function / homology
Function and homology information


DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
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 / :
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 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 21, 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_80433.png

Downloads & links

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Map

FileDownload / File: emd_80433.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 240 pix.
= 274.08 Å		1.14 Å/pix.
x 240 pix.
= 274.08 Å		1.14 Å/pix.
x 240 pix.
= 274.08 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: 0.01
Minimum - Maximum-0.001722136 - 2.2426858
Average (Standard dev.)0.00063109276 (±0.017986616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 274.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_80433_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: raw map

Fileemd_80433_additional_1.map
Annotationraw map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap1

Fileemd_80433_half_map_1.map
Annotationhalfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap2

Fileemd_80433_half_map_2.map
Annotationhalfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E. coli beta sliding clamp

EntireName: E. coli beta sliding clamp
Components
  • Complex: E. coli beta sliding clamp
    • Protein or peptide: Beta sliding clamp

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Supramolecule #1: E. coli beta sliding clamp

SupramoleculeName: E. coli beta sliding clamp / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Beta sliding clamp

MacromoleculeName: Beta sliding clamp / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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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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 / Support film - topology: HOLEY / 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
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: 34176 / 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: 3625782
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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.0) / Number images used: 89946
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: 6 / Software - Name: cryoSPARC (ver. 5.0.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-25wz:
Cryo-EM structure of the E. coli beta sliding clamp

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