[English] 日本語
Yorodumi
- EMDB-42967: CryoEM structure of AriA-AriB complex (Form II) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42967
TitleCryoEM structure of AriA-AriB complex (Form II)
Map data
Sample
  • Complex: AriAB complex
    • Protein or peptide: AriA antitoxin
    • Protein or peptide: AriB
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsBacterial Defense system / Toxin-antitoxin system / AriAB / PARIS / IMMUNE SYSTEM
Function / homology: / :
Function and homology information
Biological speciesEscherichia coli B185 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.08 Å
AuthorsDeep A / Corbett KD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM144121 United States
CitationJournal: Nature / Year: 2024
Title: Architecture and activation mechanism of the bacterial PARIS defence system.
Authors: Amar Deep / Qishan Liang / Eray Enustun / Joe Pogliano / Kevin D Corbett /
Abstract: Bacteria and their viruses (bacteriophages or phages) are engaged in an intense evolutionary arms race. While the mechanisms of many bacterial antiphage defence systems are known, how these systems ...Bacteria and their viruses (bacteriophages or phages) are engaged in an intense evolutionary arms race. While the mechanisms of many bacterial antiphage defence systems are known, how these systems avoid toxicity outside infection yet activate quickly after infection is less well understood. Here we show that the bacterial phage anti-restriction-induced system (PARIS) operates as a toxin-antitoxin system, in which the antitoxin AriA sequesters and inactivates the toxin AriB until triggered by the T7 phage counterdefence protein Ocr. Using cryo-electron microscopy, we show that AriA is related to SMC-family ATPases but assembles into a distinctive homohexameric complex through two oligomerization interfaces. In uninfected cells, the AriA hexamer binds to up to three monomers of AriB, maintaining them in an inactive state. After Ocr binding, the AriA hexamer undergoes a structural rearrangement, releasing AriB and allowing it to dimerize and activate. AriB is a toprim/OLD-family nuclease, the activation of which arrests cell growth and inhibits phage propagation by globally inhibiting protein translation through specific cleavage of a lysine tRNA. Collectively, our findings reveal the intricate molecular mechanisms of a bacterial defence system triggered by a phage counterdefence protein, and highlight how an SMC-family ATPase has been adapted as a bacterial infection sensor.
History
DepositionNov 28, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42967.png

Downloads & links

-
Map

FileDownload / File: emd_42967.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 384 pix.
= 359.04 Å		0.94 Å/pix.
x 384 pix.
= 359.04 Å		0.94 Å/pix.
x 384 pix.
= 359.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.17674856 - 0.37541056
Average (Standard dev.)-0.00029714024 (±0.0113964295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 359.04 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_42967_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_42967_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : AriAB complex

EntireName: AriAB complex
Components
  • Complex: AriAB complex
    • Protein or peptide: AriA antitoxin
    • Protein or peptide: AriB
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: AriAB complex

SupramoleculeName: AriAB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: AriA-AriB
Source (natural)Organism: Escherichia coli B185 (bacteria)
Molecular weightTheoretical: 360 KDa

-
Macromolecule #1: AriA antitoxin

MacromoleculeName: AriA antitoxin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli B185 (bacteria)
Molecular weightTheoretical: 53.287113 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VAIRTISKIE LSKIHNRYNL TVDFFNDLNV IHGKNGAGKS TLIHVIANIV NGDFIRFAFL IFEEIKATYS DGLKIVIRRD KIDEQSFIS VTLSNGKYIK FAVGEAMATV REIESERHLR ERDVKSMLAM DIDKFVKENE LQKVRASYFP AFRTMLEAWS S SSDVGYER ...String:
VAIRTISKIE LSKIHNRYNL TVDFFNDLNV IHGKNGAGKS TLIHVIANIV NGDFIRFAFL IFEEIKATYS DGLKIVIRRD KIDEQSFIS VTLSNGKYIK FAVGEAMATV REIESERHLR ERDVKSMLAM DIDKFVKENE LQKVRASYFP AFRTMLEAWS S SSDVGYER RVIRSSFYNR KASAFARELF GQFLPSINYP SPMEIEDRLR EEIRRAQLGI AAYESRTFSE SFVKVFSALF DN SSVEGEI TGELLKEIEG LAIAQDSSIK NGYYAEYSKV YEEIRSLINR NLKGKVENSV SGALVVYRDA LRDRQDYQEK AFS EIDNYM SSVNSFLEDK EMAYDFDLRR KYPKVGLKFP DGSWSPIRVL SSGERQLLTM LYAASKMGDD AIVLIDQPEI SLHI DWQED LLKRMLSQLS GRQIIVCTHS PSIATGYEDF MINISPEFIS SRDNDNHKDS EEMEEDESL

UniProtKB: UNIPROTKB: D6IC77

-
Macromolecule #2: AriB

MacromoleculeName: AriB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli B185 (bacteria)
Molecular weightTheoretical: 34.749578 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSCAYTIDS YITLLTMSSK KRLLVEGRHD RSHLYQLIYK FNPASKVKID TAQDIKASDK AMSKNNRLKI ETIHSKVKGK DNISFLCDR AFREFAFNDQ IEDLLNSHYC DDSLYWTLGH SLENYFFNPS IIIDAFQFLS PSEYKYKAIE LFSELISSSF A VLAAVSLA ...String:
MSSCAYTIDS YITLLTMSSK KRLLVEGRHD RSHLYQLIYK FNPASKVKID TAQDIKASDK AMSKNNRLKI ETIHSKVKGK DNISFLCDR AFREFAFNDQ IEDLLNSHYC DDSLYWTLGH SLENYFFNPS IIIDAFQFLS PSEYKYKAIE LFSELISSSF A VLAAVSLA AKDIDKAGLP AALIDWKDIV INDGTIKLIR RDSYDIDSAC VDSFFNAFDA VLPRVIASDV GICSRVVRGH TG ILLLQKL FSACLYYVGR EDDALQADSS ANYFCNLSEL SLTTALAESW VRKIGVLEDV YFPDSLLKNI E

UniProtKB: UNIPROTKB: D6IC76

-
Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
250.0 mMNaClSodium chloride
20.0 mMTristris(hydroxymethyl)aminomethane
2.0 mMBME2-Mercaptoethanol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 12 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5058 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22415
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8v47:
CryoEM structure of AriA-AriB complex (Form II)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more