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- PDB-8dgf: Avs4 bound to phage PhiV-1 portal -

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Basic information

Entry
Database: PDB / ID: 8dgf
TitleAvs4 bound to phage PhiV-1 portal
Components
  • ATP-binding protein Avs4
  • Portal protein
KeywordsANTIVIRAL PROTEIN / phage defense / pattern-recognition receptor / nlr / stand / atpase
Function / homologyPortal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / ADENOSINE-5'-TRIPHOSPHATE / Portal protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Escherichia phage PhiV-1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWilkinson, M.E. / Gao, L. / Strecker, J. / Makarova, K.S. / Macrae, R.K. / Koonin, E.V. / Zhang, F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5DP1HL141201-04 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)2R01HG009761-05 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2022
Title: Prokaryotic innate immunity through pattern recognition of conserved viral proteins.
Authors: Linyi Alex Gao / Max E Wilkinson / Jonathan Strecker / Kira S Makarova / Rhiannon K Macrae / Eugene V Koonin / Feng Zhang /
Abstract: Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in ...Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in plants, animals, and fungi. Although the roles of NLRs in eukaryotic immunity are well established, it is unknown whether prokaryotes use similar defense mechanisms. Here, we show that antiviral STAND (Avs) homologs in bacteria and archaea detect hallmark viral proteins, triggering Avs tetramerization and the activation of diverse N-terminal effector domains, including DNA endonucleases, to abrogate infection. Cryo-electron microscopy reveals that Avs sensor domains recognize conserved folds, active-site residues, and enzyme ligands, allowing a single Avs receptor to detect a wide variety of viruses. These findings extend the paradigm of pattern recognition of pathogen-specific proteins across all three domains of life.
History
DepositionJun 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-binding protein Avs4
B: ATP-binding protein Avs4
C: ATP-binding protein Avs4
D: ATP-binding protein Avs4
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)982,91416
Polymers980,7888
Non-polymers2,1268
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
ATP-binding protein Avs4


Mass: 186640.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: NCTC11132 / Production host: Escherichia coli (E. coli)
#2: Protein
Portal protein / Head-to-tail connector / gp8 portal


Mass: 58556.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage PhiV-1 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G3WWQ5
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY
Has protein modificationY

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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: Avs4 bound to phage PhiV-1 portal / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.98 MDa / Experimental value: NO
Buffer solutionpH: 7.4
SpecimenConc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 31 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20_4459: / Classification: refinement
EM softwareName: RELION / Version: 4 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169977 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00966394
ELECTRON MICROSCOPYf_angle_d1.20189788
ELECTRON MICROSCOPYf_dihedral_angle_d6.2678624
ELECTRON MICROSCOPYf_chiral_restr0.069842
ELECTRON MICROSCOPYf_plane_restr0.00911402

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