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- EMDB-49243: Helical assembly of AVAST5 filament -

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Basic information

Entry
Database: EMDB / ID: EMD-49243
TitleHelical assembly of AVAST5 filament
Map data
Sample
  • Complex: Helical assembly of AVAST5 filament
    • Protein or peptide: SIR2 family protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsanti-phage / innate immunity / inflammasome / ATPase / SIR2 domain / filament / helical assembly / NADase / IMMUNE SYSTEM
Function / homologySIR2-like domain / SIR2 family protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsShen Z / Xie J / Fu TM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Helical assembly of AVAST5 filament
Authors: Shen Z / Xie J / Fu TM
History
DepositionFeb 15, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49243.png

Downloads & links

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Map

FileDownload / File: emd_49243.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 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: 0.106
Minimum - Maximum-0.3754533 - 0.8154686
Average (Standard dev.)0.0015228193 (±0.030723713)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_49243_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49243_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_49243_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 : Helical assembly of AVAST5 filament

EntireName: Helical assembly of AVAST5 filament
Components
  • Complex: Helical assembly of AVAST5 filament
    • Protein or peptide: SIR2 family protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Helical assembly of AVAST5 filament

SupramoleculeName: Helical assembly of AVAST5 filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: SIR2 family protein

MacromoleculeName: SIR2 family protein / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 89.252258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQVQHHTEPN LKNEIVALFK ASQLIPFFGS GFTRDIRAKN GKVPDAIKFT ELIRNIAAEK EGLTQTEIDE ILRISQLKKA FGLLNMEEY IPKRKSKALL GNIFSECKLS DHEKTKIINL DWPHIFTFNI DDAIENVNRK YKILHPNRAV QREFISANKC L FKIHGDIT ...String:
MQVQHHTEPN LKNEIVALFK ASQLIPFFGS GFTRDIRAKN GKVPDAIKFT ELIRNIAAEK EGLTQTEIDE ILRISQLKKA FGLLNMEEY IPKRKSKALL GNIFSECKLS DHEKTKIINL DWPHIFTFNI DDAIENVNRK YKILHPNRAV QREFISANKC L FKIHGDIT EFIKYEDQNL IFTWREYAHS IEENKSMLSF LSEEAKNSAF LFIGCSLDGE LDLMHLSRST PFKKSIYLKK GY LNLEEKI ALSEYGIEKV ITFDTYDQIY QWLNNTLQNV ERKSPTRSFE LDDSKLMKEE AINLFANGGP VTKIVDNKRI LRN SITFSQ RDVCDDAIKA LRNHDYILIT GRRFSGKSVL LFQIIEAKKE YNASYYSSTD TFDPSIKNSL IKFENHIFVF DSNF FNAQS IDEILTTRVH PSNKVVLCSS FGDAELYRFK LKDKKILHTE IQIKNNLINE EGNYLNDKLS FEGLPLYKSS ETLLN FAYR YYSEYKNRLS GSNLFNKQFD EDSMFVLILI AAFNKATYGH INSHNKYFDI QNFISQNDRL FELESTNTDP SGVIIC NSP SWLLRVISEY IDKNPASYKT VSDLIISLAS KGFLAASRNL ISFDKLNELG NGKNVHKFIR GIYKEIAHTY REDMHYW LQ RAKSELISAH TIDDLVEGMS YASKVRLDSA EFKNQTYYSA TLVLAQLSAR ALSINNDKIY ALSFFESSLE SIRNYNNN S RHINKMMDKN DGGFRYAIQY LKDNPLIELL PRKDEVNELI NFYESRKK

UniProtKB: SIR2 family protein

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 11 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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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

Final reconstructionApplied symmetry - Helical parameters - Δz: 39.74 Å
Applied symmetry - Helical parameters - Δ&Phi: 142.35 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107279
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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