5FKW | pdb_00005fkw

cryo-EM structure of the E. coli replicative DNA polymerase complex bound to DNA (DNA polymerase III alpha, beta, epsilon)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

cryo-EM structures of theE. colireplicative DNA polymerase reveal its dynamic interactions with the DNA sliding clamp, exonuclease andtau.

Fernandez-Leiro, R.Conrad, J.Scheres, S.H.Lamers, M.H.

(2015) Elife 4

  • DOI: https://doi.org/10.7554/eLife.11134
  • Primary Citation Related Structures: 
    5FKU, 5FKV, 5FKW

  • PubMed Abstract: 

    The replicative DNA polymerase PolIIIα from Escherichia coli is a uniquely fast and processive enzyme. For its activity it relies on the DNA sliding clamp β, the proofreading exonuclease ε and the C-terminal domain of the clamp loader subunit τ. Due to the dynamic nature of the four-protein complex it has long been refractory to structural characterization. Here we present the 8 Å resolution cryo-electron microscopy structures of DNA-bound and DNA-free states of the PolIII-clamp-exonuclease-τ c complex. The structures show how the polymerase is tethered to the DNA through multiple contacts with the clamp and exonuclease. A novel contact between the polymerase and clamp is made in the DNA bound state, facilitated by a large movement of the polymerase tail domain and τ c . These structures provide crucial insights into the organization of the catalytic core of the replisome and form an important step towards determining the structure of the complete holoenzyme.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 255.06 kDa 
  • Atom Count: 15,726 
  • Modeled Residue Count: 1,929 
  • Deposited Residue Count: 2,189 
  • Unique protein chains: 3
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA POLYMERASE III ALPHA1,160Escherichia coli K-12Mutation(s): 2 
EC: 2.7.7.7
UniProt
Find proteins for P10443 (Escherichia coli (strain K12))
Explore P10443 
Go to UniProtKB:  P10443
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UniProt GroupP10443
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA POLYMERASE III BETA
B, C
366Escherichia coli K-12Mutation(s): 0 
EC: 2.7.7.7
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: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA POLYMERASE III EPSILON243Escherichia coli K-12Mutation(s): 4 
EC: 2.7.7.7
UniProt
Find proteins for P03007 (Escherichia coli (strain K12))
Explore P03007 
Go to UniProtKB:  P03007
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UniProt GroupP03007
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
PRIMER-TEMPLATE DUPLEX DNAE [auth P]25synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
PRIMER-TEMPLATE DUPLEX DNAF [auth T]29synthetic construct
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2017-04-19
    Changes: Other
  • Version 1.3: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references