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- PDB-9rp3: Structure of Avast type 5 activator (Gp316, JADA jumbophage protein) -

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Basic information

Entry
Database: PDB / ID: 9rp3
TitleStructure of Avast type 5 activator (Gp316, JADA jumbophage protein)
ComponentsGp316/JADA
KeywordsUNKNOWN FUNCTION / jumbophage / gp316 / jada / avast5 / dimer
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPseudomonas phage vB_PA32_GUMS (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsPacesa, M. / Muralidharan, A. / Brouns, S.J.J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101003229European Union
CitationJournal: To Be Published
Title: Molecular basis for anti-jumbo phage immunity by AVAST Type V
Authors: Muralidharan, A. / Rita Costa, A. / Fierlier, D. / van den Berg, D.F. / van den Bossche, H. / Zoumaro-Djayoon, A. / Pabst, M. / Pacesa, M. / Correia, B.E. / Brouns, S.J.J.
History
DepositionJun 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gp316/JADA
B: Gp316/JADA


Theoretical massNumber of molelcules
Total (without water)160,4232
Polymers160,4232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Gp316/JADA


Mass: 80211.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage vB_PA32_GUMS (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T8BGC1
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: Gp316/JADA homodimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas phage vB_PA32_GUMS (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15624
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1723569 / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE

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