7BTP

EcoR124I-Ocr in Restriction-Alleviation State


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into assembly, operation and inhibition of a type I restriction-modification system.

Gao, Y.Cao, D.Zhu, J.Feng, H.Luo, X.Liu, S.Yan, X.X.Zhang, X.Gao, P.

(2020) Nat Microbiol 5: 1107-1118

  • DOI: https://doi.org/10.1038/s41564-020-0731-z
  • Primary Citation of Related Structures:  
    7BST, 7BTO, 7BTP, 7BTQ, 7BTR

  • PubMed Abstract: 

    Type I restriction-modification (R-M) systems are widespread in prokaryotic genomes and provide robust protection against foreign DNA. They are multisubunit enzymes with methyltransferase, endonuclease and translocase activities. Despite extensive studies over the past five decades, little is known about the molecular mechanisms of these sophisticated machines. Here, we report the cryo-electron microscopy structures of the representative EcoR124I R-M system in different assemblies (R 2 M 2 S 1 , R 1 M 2 S 1 and M 2 S 1 ) bound to target DNA and the phage and mobile genetic element-encoded anti-restriction proteins Ocr and ArdA. EcoR124I can precisely regulate different enzymatic activities by adopting distinct conformations. The marked conformational transitions of EcoR124I are dependent on the intrinsic flexibility at both the individual-subunit and assembled-complex levels. Moreover, Ocr and ArdA use a DNA-mimicry strategy to inhibit multiple activities, but do not block the conformational transitions of the complexes. These structural findings, complemented by mutational studies of key intermolecular contacts, provide insights into assembly, operation and inhibition mechanisms of type I R-M systems.


  • Organizational Affiliation

    CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type-1 restriction enzyme EcoR124II specificity proteinA [auth E]404Escherichia coliMutation(s): 0 
Gene Names: hsdShss
UniProt
Find proteins for P10485 (Escherichia coli)
Explore P10485 
Go to UniProtKB:  P10485
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UniProt GroupP10485
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Type I restriction enzyme R ProteinB [auth A]1,038Escherichia coliMutation(s): 0 
Gene Names: hsdR
EC: 3.1.21.3
UniProt
Find proteins for P10486 (Escherichia coli)
Explore P10486 
Go to UniProtKB:  P10486
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UniProt GroupP10486
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Type I restriction enzyme EcoR124II M proteinC [auth B],
D [auth C]
520Escherichia coliMutation(s): 0 
Gene Names: hsdMhsm
EC: 2.1.1.72
UniProt
Find proteins for P10484 (Escherichia coli)
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Go to UniProtKB:  P10484
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UniProt GroupP10484
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Overcome classical restriction gp0.3E [auth D],
F
117Escherichia phage T7Mutation(s): 0 
Gene Names: 0.3
UniProt
Find proteins for P03775 (Escherichia phage T7)
Explore P03775 
Go to UniProtKB:  P03775
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UniProt GroupP03775
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.01 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: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-06-24
    Changes: Database references
  • Version 1.2: 2020-09-09
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references