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- EMDB-71020: Focus refined map of E. coli clamp loader sub-complex Psi-Chi -

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Basic information

Entry
Database: EMDB / ID: EMD-71020
TitleFocus refined map of E. coli clamp loader sub-complex Psi-Chi
Map datafocused map
Sample
  • Complex: E. coli clamp loading complex
    • Complex: E. coli clamp loader sub-complex Psi-Chi
      • Protein or peptide: E. coli clamp loader sub-complex Psi-Chi
    • Complex: 10-nt gapped DNA substrate
KeywordsE. Coli / DNA replication / DNA damage repair / clamp loading complex / clamp beta / clamp loader DnaX-complex / REPLICATION
Biological speciesEscherichia coli (E. coli) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsZheng F / Yao YN / Georgescu R / O'Donnell ME / Li H
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115809 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mol Cell / Year: 2026
Title: The E. coli DnaX clamp loader sharply bends DNA to load β-clamp at nicks and small gaps.
Authors: Fengwei Zheng / Nina Y Yao / Roxana E Georgescu / Meinan Lyu / Michael E O'Donnell / Huilin Li /
Abstract: DNA sliding clamps are essential for processive DNA synthesis in all domains of life and are loaded by ATP-dependent clamp loaders that recognize recessed 3' ends. How clamp loaders function at nicks ...DNA sliding clamps are essential for processive DNA synthesis in all domains of life and are loaded by ATP-dependent clamp loaders that recognize recessed 3' ends. How clamp loaders function at nicks and small single-stranded DNA (ssDNA) gaps-common DNA repair intermediates-remains unclear. Here, we show that the bacterial E. coli DnaX clamp loader uses a mechanism distinct from its eukaryotic counterpart. Whereas eukaryotic replication factor C (RFC) unwinds DNA at the recessed 3' end and stabilizes the 5'-dsDNA (double-stranded DNA) at a shoulder site, the bacterial DnaX-complex neither unwinds DNA nor stably binds the 5'-dsDNA in vitro. Instead, cryo-EM structures reveal that the β-clamp contains a conserved external DNA-binding site that bends gapped DNA by ∼150°, promoting insertion of 3'-dsDNA into the clamp. This DNA-bending mechanism enables efficient β-clamp loading at nicks and small gaps and reveals a distinct bacterial strategy likely important for DNA repair.
History
DepositionJun 4, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71020.png

Downloads & links

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Map

FileDownload / File: emd_71020.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfocused map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.9612365 - 3.4844575
Average (Standard dev.)-0.0008431627 (±0.030080378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_71020_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_71020_half_map_2.map
Annotationhalf map B
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 clamp loading complex

EntireName: E. coli clamp loading complex
Components
  • Complex: E. coli clamp loading complex
    • Complex: E. coli clamp loader sub-complex Psi-Chi
      • Protein or peptide: E. coli clamp loader sub-complex Psi-Chi
    • Complex: 10-nt gapped DNA substrate

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Supramolecule #1: E. coli clamp loading complex

SupramoleculeName: E. coli clamp loading complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11

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Supramolecule #2: E. coli clamp loader sub-complex Psi-Chi

SupramoleculeName: E. coli clamp loader sub-complex Psi-Chi / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#7, #10
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: 10-nt gapped DNA substrate

SupramoleculeName: 10-nt gapped DNA substrate / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8-#9, #11
Source (natural)Organism: DNA molecule (others)

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Macromolecule #1: E. coli clamp loader sub-complex Psi-Chi

MacromoleculeName: E. coli clamp loader sub-complex Psi-Chi / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: SRRDWQLQQL GITQWSLRRP GALQGEIAIA IPAHVRLVMV ANDLPALTDP LVSDVLRALT VSPDQVLQLT PEKIAMLPQG SHCNSWRLG TDEPLSLEGA QVASPALTDL RANPTARAAL WQQICTYEHD FFPKNATFYL LDNDTTVDGL SAVEQLVCEI AAERWRSGKR ...String:
SRRDWQLQQL GITQWSLRRP GALQGEIAIA IPAHVRLVMV ANDLPALTDP LVSDVLRALT VSPDQVLQLT PEKIAMLPQG SHCNSWRLG TDEPLSLEGA QVASPALTDL RANPTARAAL WQQICTYEHD FFPKNATFYL LDNDTTVDGL SAVEQLVCEI AAERWRSGKR VLIACEDEKQ AYRLDEALWA RPAESFVPHN LAGEGPRGGA PVE IAWPQK RSSSRRDILI SLRTSFADFA TAFTEVVDFV PYEDSLKQLA RERYKAYRVA GFNLNTATWK

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.6 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3sxu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242505
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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