8VAL

Structure of the E. coli clamp loader bound to the beta clamp in a Open-DNAp/t conformation


Experimental Data Snapshot

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

Starting Models: experimental
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This is version 1.1 of the entry. See complete history


Literature

Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication.

Landeck, J.T.Pajak, J.Norman, E.K.Sedivy, E.L.Kelch, B.A.

(2024) J Biol Chem 300: 107166-107166

  • DOI: https://doi.org/10.1016/j.jbc.2024.107166
  • Primary Citation of Related Structures:  
    8VAL, 8VAM, 8VAN, 8VAP, 8VAQ, 8VAR, 8VAS, 8VAT

  • PubMed Abstract: 

    Clamp loaders are pentameric ATPases that place circular sliding clamps onto DNA, where they function in DNA replication and genome integrity. The central activity of a clamp loader is the opening of the ring-shaped sliding clamp and the subsequent binding to primer-template (p/t)-junctions. The general architecture of clamp loaders is conserved across all life, suggesting that their mechanism is retained. Recent structural studies of the eukaryotic clamp loader replication factor C (RFC) revealed that it functions using a crab-claw mechanism, where clamp opening is coupled to a massive conformational change in the loader. Here we investigate the clamp loading mechanism of the Escherichia coli clamp loader at high resolution using cryo-electron microscopy. We find that the E. coli clamp loader opens the clamp using a crab-claw motion at a single pivot point, whereas the eukaryotic RFC loader uses motions distributed across the complex. Furthermore, we find clamp opening occurs in multiple steps, starting with a partly open state with a spiral conformation, and proceeding to a wide open clamp in a surprising planar geometry. Finally, our structures in the presence of p/t-junctions illustrate how the clamp closes around p/t-junctions and how the clamp loader initiates release from the loaded clamp. Our results reveal mechanistic distinctions in a macromolecular machine that is conserved across all domains of life.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase III subunit delta343Escherichia coliMutation(s): 0 
Gene Names: holA
EC: 2.7.7.7
UniProt
Find proteins for P28630 (Escherichia coli (strain K12))
Explore P28630 
Go to UniProtKB:  P28630
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28630
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
376Escherichia coliMutation(s): 0 
Gene Names: dnaXdnaZdnaZXb0470JW0459
EC: 2.7.7.7
UniProt
Find proteins for P06710 (Escherichia coli (strain K12))
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Go to UniProtKB:  P06710
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UniProt GroupP06710
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase III subunit delta'337Escherichia coliMutation(s): 0 
Gene Names: holB
EC: 2.7.7.7
UniProt
Find proteins for P28631 (Escherichia coli (strain K12))
Explore P28631 
Go to UniProtKB:  P28631
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UniProt GroupP28631
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta sliding clamp
F, G
369Escherichia coliMutation(s): 0 
Gene Names: dnaN
UniProt
Find proteins for P0A988 (Escherichia coli (strain K12))
Explore P0A988 
Go to UniProtKB:  P0A988
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UniProt GroupP0A988
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*AP*CP*AP*CP*TP*AP*CP*GP*AP*GP*TP*AP*CP*AP*TP*A)-3')20synthetic construct
Sequence Annotations
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*AP*TP*GP*TP*AP*CP*TP*CP*GP*TP*AP*GP*TP*GP*TP*CP*T)-3')30synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
K [auth B],
O [auth C],
S [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF (Subject of Investigation/LOI)
Query on BEF

Download Ideal Coordinates CCD File 
L [auth B],
P [auth C],
T [auth D]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
J [auth B],
N [auth C],
R [auth D],
V [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
M [auth B],
Q [auth C],
U [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
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127776
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM145943

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references