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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: To Be Published
Title: The E. coli clamp loader sharply bends DNA to load beta-clamp onto small gaps
Authors: Zheng F / Yao YN / Georgescu R / Lyu M / O'Donnell ME / Li H
History
DepositionJun 4, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 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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