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- EMDB-42968: CryoEM structure of AriA-AriB complex (Form III) -

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Basic information

Entry
Database: EMDB / ID: EMD-42968
TitleCryoEM structure of AriA-AriB complex (Form III)
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: 3.68 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: To Be Published
Title: CryoEM structure of AriA-AriB complex (Form III)
Authors: Deep A / Corbett KD
History
DepositionNov 28, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42968.png

Downloads & links

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Map

FileDownload / File: emd_42968.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: 0.06
Minimum - Maximum-0.2495876 - 0.55579114
Average (Standard dev.)-0.00025562276 (±0.012725267)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_42968_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_42968_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AriAB complex

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

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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: 390 KDa

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Macromolecule #1: AriA antitoxin

MacromoleculeName: AriA antitoxin / type: protein_or_peptide / ID: 1 / Number of copies: 6 / 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

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Macromolecule #2: AriB

MacromoleculeName: AriB / type: protein_or_peptide / ID: 2 / Number of copies: 3 / 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

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24138
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8v48:
CryoEM structure of AriA-AriB complex (Form III)

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