8GIY

E. coli clamp loader with closed clamp


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural characterisation of the complete cycle of sliding clamp loading in Escherichia coli.

Xu, Z.Q.Jergic, S.Lo, A.T.Y.Pradhan, A.C.Brown, S.H.J.Bouwer, J.C.Ghodke, H.Lewis, P.J.Tolun, G.Oakley, A.J.Dixon, N.E.

(2024) Nat Commun 15: 8372-8372

  • DOI: https://doi.org/10.1038/s41467-024-52623-9
  • Primary Citation of Related Structures:  
    8GIY, 8GIZ, 8GJ0, 8GJ1, 8GJ2, 8GJ3

  • PubMed Abstract: 

    Ring-shaped DNA sliding clamps are essential for DNA replication and genome maintenance. Clamps need to be opened and chaperoned onto DNA by clamp loader complexes (CLCs). Detailed understanding of the mechanisms by which CLCs open and place clamps around DNA remains incomplete. Here, we present a series of six structures of the Escherichia coli CLC bound to an open or closed clamp prior to and after binding to a primer-template DNA, representing the most significant intermediates in the clamp loading process. We show that the ATP-bound CLC first binds to a clamp, then constricts to hold onto it. The CLC then expands to open the clamp with a gap large enough for double-stranded DNA to enter. Upon binding to DNA, the CLC constricts slightly, allowing clamp closing around DNA. These structures provide critical high-resolution snapshots of clamp loading by the E. coli CLC, revealing how the molecular machine works.


  • Organizational Affiliation

    Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia. zhiqiang@uow.edu.au.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase III subunit delta343Escherichia coli K-12Mutation(s): 0 
Gene Names: holAb0640JW0635
EC: 2.7.7.7
UniProt
Find proteins for P28630 (Escherichia coli (strain K12))
Go to UniProtKB:  P28630
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase III subunit tau
B, C, D
431Escherichia coli K-12Mutation(s): 0 
Gene Names: dnaXdnaZdnaZXb0470JW0459
EC: 2.7.7.7
UniProt
Find proteins for P06710 (Escherichia coli (strain K12))
Go to UniProtKB:  P06710
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase III subunit delta'334Escherichia coli K-12Mutation(s): 0 
Gene Names: holBb1099JW1085
EC: 2.7.7.7
UniProt
Find proteins for P28631 (Escherichia coli (strain K12))
Go to UniProtKB:  P28631
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase III subunit psi137Escherichia coli K-12Mutation(s): 0 
Gene Names: holDb4372JW4334
EC: 2.7.7.7
UniProt
Find proteins for P28632 (Escherichia coli (strain K12))
Go to UniProtKB:  P28632
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Beta sliding clampG [auth H],
H [auth I]
366Escherichia coli K-12Mutation(s): 0 
Gene Names: dnaNb3701JW3678
UniProt
Find proteins for P0A988 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A988
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
I [auth B],
L [auth C],
O [auth D]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
K [auth B],
N [auth C],
Q [auth D],
R [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth B],
M [auth C],
P [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXdev-4788
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP210100365

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary