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- PDB-7btp: EcoR124I-Ocr in Restriction-Alleviation State -

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Basic information

Entry
Database: PDB / ID: 7btp
TitleEcoR124I-Ocr in Restriction-Alleviation State
Components
  • Overcome classical restriction gp0.3
  • Type I restriction enzyme EcoR124II M protein
  • Type I restriction enzyme R Protein
  • Type-1 restriction enzyme EcoR124II specificity protein
KeywordsIMMUNE SYSTEM / Cryoelectron microscopy / Innate immune mechanism / Complex
Function / homology
Function and homology information


type I site-specific deoxyribonuclease / type I site-specific deoxyribonuclease activity / symbiont-mediated evasion of host restriction-modification system / N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / DNA binding / ATP binding
Similarity search - Function
B-form DNA mimic Ocr / DNA mimic ocr / Protein Ocr / Restriction endonuclease, type I, methylase subunit / Type I restriction modification DNA specificity domain superfamily / Restriction endonuclease, type I, HsdR, N-terminal / Type I restriction enzyme R protein, C-terminal / SWI2/SNF2 ATPase / Type I restriction modification DNA specificity domain / Type I restriction enzyme R protein N terminus (HSDR_N) ...B-form DNA mimic Ocr / DNA mimic ocr / Protein Ocr / Restriction endonuclease, type I, methylase subunit / Type I restriction modification DNA specificity domain superfamily / Restriction endonuclease, type I, HsdR, N-terminal / Type I restriction enzyme R protein, C-terminal / SWI2/SNF2 ATPase / Type I restriction modification DNA specificity domain / Type I restriction enzyme R protein N terminus (HSDR_N) / Type I restriction and modification enzyme - subunit R C terminal / SWI2/SNF2 ATPase / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / HsdM N-terminal domain / Type I restriction modification DNA specificity domain / Restriction endonuclease, type I, HsdR / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein Ocr / Type I restriction enzyme EcoR124I/EcoR124II methylase subunit / Type I restriction enzyme EcoR124I/EcoR124II specificity subunit / Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit / Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.01 Å
AuthorsGao, Y. / Gao, P.
CitationJournal: Nat Microbiol / Year: 2020
Title: Structural insights into assembly, operation and inhibition of a type I restriction-modification system.
Authors: Yina Gao / Duanfang Cao / Jingpeng Zhu / Han Feng / Xiu Luo / Songqing Liu / Xiao-Xue Yan / Xinzheng Zhang / Pu Gao /
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, ...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 (RMS, RMS and MS) 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.
History
DepositionApr 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
E: Type-1 restriction enzyme EcoR124II specificity protein
A: Type I restriction enzyme R Protein
B: Type I restriction enzyme EcoR124II M protein
C: Type I restriction enzyme EcoR124II M protein
D: Overcome classical restriction gp0.3
F: Overcome classical restriction gp0.3


Theoretical massNumber of molelcules
Total (without water)310,3076
Polymers310,3076
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15650 Å2
ΔGint-48 kcal/mol
Surface area124650 Å2

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Components

#1: Protein Type-1 restriction enzyme EcoR124II specificity protein / S.EcoR124II / Type I restriction enzyme EcoR124II specificity protein / S protein


Mass: 46235.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hsdS, hss / Production host: Escherichia coli (E. coli) / References: UniProt: P10485
#2: Protein Type I restriction enzyme R Protein


Mass: 120278.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hsdR / Production host: Escherichia coli (E. coli)
References: UniProt: Q304R3, UniProt: P10486*PLUS, type I site-specific deoxyribonuclease
#3: Protein Type I restriction enzyme EcoR124II M protein / M.EcoR124II


Mass: 58077.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hsdM, hsm / Production host: Escherichia coli (E. coli)
References: UniProt: P10484, site-specific DNA-methyltransferase (adenine-specific)
#4: Protein Overcome classical restriction gp0.3 / Gene product 0.3 / Gp0.3 / OCR


Mass: 13819.015 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T7 (virus) / Gene: 0.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P03775

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: EcoR124I-Ocr / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197498 / Symmetry type: POINT

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