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- PDB-9nah: Monomeric AVAST5 binds a SIR2 domain -

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Basic information

Entry
Database: PDB / ID: 9nah
TitleMonomeric AVAST5 binds a SIR2 domain
ComponentsSIR2 family protein
KeywordsIMMUNE SYSTEM / ATPase / AVAST / Antiviral / SIR2 / E. coli / prokaryotic / Innate Immunity / Inflammasome / Filament
Function / homologySIR2-like domain / ADENOSINE-5'-TRIPHOSPHATE / SIR2 family protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsXie, J. / Wang, C. / Fu, T.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Monomeric AVAST5 binds an SIR2 domain
Authors: Xie, J. / Fu, T.M.
History
DepositionFeb 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIR2 family protein
C: SIR2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,0123
Polymers178,5052
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein SIR2 family protein


Mass: 89252.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FPI65_07120 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6N9S4L0
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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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: AVS5 bound to a SIR2 domain / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 51.5 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1EPUparticle selection
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143403 / Symmetry type: POINT
RefinementHighest resolution: 3.64 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027314
ELECTRON MICROSCOPYf_angle_d0.6310001
ELECTRON MICROSCOPYf_dihedral_angle_d5.4441068
ELECTRON MICROSCOPYf_chiral_restr0.0411226
ELECTRON MICROSCOPYf_plane_restr0.0041280

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