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- EMDB-49598: Dimeric E. coli AVAST5 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-49598
TitleDimeric E. coli AVAST5
Map data
Sample
  • Complex: Monomeric AVAST5 bound to a SIR2 domain
    • Protein or peptide: AVAST5
KeywordsATPase / AVAST / Antiviral / SIR2 / E. coli / prokaryotic / Innate Immunity / Inflammasome / Filament / IMMUNE SYSTEM
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsShen Z / Xie J / Fu TM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Monomeric AVAST5 binds an SIR2 domain
Authors: Shen Z / Xie J / Fu TM
History
DepositionMar 9, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49598.png

Downloads & links

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Map

FileDownload / File: emd_49598.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.3431937 - 0.69322336
Average (Standard dev.)0.00034369683 (±0.01753325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_49598_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49598_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49598_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 : Monomeric AVAST5 bound to a SIR2 domain

EntireName: Monomeric AVAST5 bound to a SIR2 domain
Components
  • Complex: Monomeric AVAST5 bound to a SIR2 domain
    • Protein or peptide: AVAST5

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Supramolecule #1: Monomeric AVAST5 bound to a SIR2 domain

SupramoleculeName: Monomeric AVAST5 bound to a SIR2 domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: AVAST5

MacromoleculeName: AVAST5 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString: MQVQHHTEPN LKNEIVALFK ASQLIPFFGS GFTRDIRAKN GKVPDAIKFT ELIRNIAAEK EGLTQTEIDE ILRISQLKKA FGLLNMEEYI PKRKSKALLG NIFSECKLSD HEKTKIINLD WPHIFTFNID DAIENVNRKY KILHPNRAVQ REFISANKCL FKIHGDITEF ...String:
MQVQHHTEPN LKNEIVALFK ASQLIPFFGS GFTRDIRAKN GKVPDAIKFT ELIRNIAAEK EGLTQTEIDE ILRISQLKKA FGLLNMEEYI PKRKSKALLG NIFSECKLSD HEKTKIINLD WPHIFTFNID DAIENVNRKY KILHPNRAVQ REFISANKCL FKIHGDITEF IKYEDQNLIF TWREYAHSIE ENKSMLSFLS EEAKNSAFLF IGCSLDGELD LMHLSRSTPF KKSIYLKKGY LNLEEKIALS EYGIEKVITF DTYDQIYQWL NNTLQNVERK SPTRSFELDD SKLMKEEAIN LFANGGPVTK IVDNKRILRN SITFSQRDVC DDAIKALRNH DYILITGRRF SGKSVLLFQI IEAKKEYNAS YYSSTDTFDP SIKNSLIKFE NHIFVFDSNF FNAQSIDEIL TTRVHPSNKV VLCSSFGDAE LYRFKLKDKK ILHTEIQIKN NLINEEGNYL NDKLSFEGLP LYKSSETLLN FAYRYYSEYK NRLSGSNLFN KQFDEDSMFV LILIAAFNKA TYGHINSHNK YFDIQNFISQ NDRLFELEST NTDPSGVIIC NSPSWLLRVI SEYIDKNPAS YKTVSDLIIS LASKGFLAAS RNLISFDKLN ELGNGKNVHK FIRGIYKEIA HTYREDMHYW LQRAKSELIS AHTIDDLVEG MSYASKVRLD SAEFKNQTYY SATLVLAQLS ARALSINNDK IYALSFFESS LESIRNYNNN SRHINKMMDK NDGGFRYAIQ YLKDNPLIEL LPRKDEVNEL INFYESRKK

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44679
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: RANDOM ASSIGNMENT

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