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- PDB-8saj: Mycobacterium phage Adjutor -

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Basic information

Entry
Database: PDB / ID: 8saj
TitleMycobacterium phage Adjutor
Components
  • HNH endonuclease
  • Major capsid protein
  • gp_16 (Minor Capsid Protein)
KeywordsVIRUS / T=7 / HK97 / Tailed bacteriophage / Capsid
Function / homologyUncharacterized protein / Capsid decoration protein / Major capsid protein
Function and homology information
Biological speciesMycobacterium phage Adjutor (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsPodgorski, J.M. / White, S.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Stabilization mechanism accommodating genome length variation in evolutionarily related viral capsids.
Authors: Jennifer M Podgorski / Joshua Podgorski / Lawrence Abad / Deborah Jacobs-Sera / Krista G Freeman / Colin Brown / Graham F Hatfull / Antoni Luque / Simon J White /
Abstract: Tailed bacteriophages are one of the most numerous and diverse group of viruses. They store their genome at quasi-crystalline densities in capsids built from multiple copies of proteins adopting the ...Tailed bacteriophages are one of the most numerous and diverse group of viruses. They store their genome at quasi-crystalline densities in capsids built from multiple copies of proteins adopting the HK97-fold. The high density of the genome exerts an internal pressure, requiring a maturation process that reinforces their capsids. However, it is unclear how capsid stabilization strategies have adapted to accommodate the evolution of larger genomes in this virus group. Here we characterize a capsid reinforcement mechanism in two evolutionary-related actinobacteriophages that modifies the length of a stabilization protein to accommodate a larger genome while maintaining the same capsid size. We use cryo-EM to reveal that capsids contain split hexamers of HK97-fold proteins with a stabilization protein in the chasm. The observation of split hexamers in mature capsids is unprecedented, so we rationalize this result mathematically, discovering that icosahedral capsids can be formed by all split or skewed hexamers as long as their T-number is not a multiple of three. Our results suggest that analogous stabilization mechanisms can be present in other icosahedral capsids, and they provide a strategy for engineering capsids accommodating larger DNA cargoes as gene delivery systems.
History
DepositionApr 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
3: gp_16 (Minor Capsid Protein)
2: gp_16 (Minor Capsid Protein)
1: gp_16 (Minor Capsid Protein)
Y: HNH endonuclease
Z: HNH endonuclease
6: gp_16 (Minor Capsid Protein)
5: gp_16 (Minor Capsid Protein)
4: gp_16 (Minor Capsid Protein)
7: gp_16 (Minor Capsid Protein)


Theoretical massNumber of molelcules
Total (without water)427,44016
Polymers427,44016
Non-polymers00
Water00
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
3: gp_16 (Minor Capsid Protein)
2: gp_16 (Minor Capsid Protein)
1: gp_16 (Minor Capsid Protein)
Y: HNH endonuclease
Z: HNH endonuclease
6: gp_16 (Minor Capsid Protein)
5: gp_16 (Minor Capsid Protein)
4: gp_16 (Minor Capsid Protein)
7: gp_16 (Minor Capsid Protein)
x 60


Theoretical massNumber of molelcules
Total (without water)25,646,411960
Polymers25,646,411960
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
3: gp_16 (Minor Capsid Protein)
2: gp_16 (Minor Capsid Protein)
1: gp_16 (Minor Capsid Protein)
Y: HNH endonuclease
Z: HNH endonuclease
6: gp_16 (Minor Capsid Protein)
5: gp_16 (Minor Capsid Protein)
4: gp_16 (Minor Capsid Protein)
7: gp_16 (Minor Capsid Protein)
x 5


  • icosahedral pentamer
  • 2.14 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)2,137,20180
Polymers2,137,20180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
3: gp_16 (Minor Capsid Protein)
2: gp_16 (Minor Capsid Protein)
1: gp_16 (Minor Capsid Protein)
Y: HNH endonuclease
Z: HNH endonuclease
6: gp_16 (Minor Capsid Protein)
5: gp_16 (Minor Capsid Protein)
4: gp_16 (Minor Capsid Protein)
7: gp_16 (Minor Capsid Protein)
x 6


  • icosahedral 23 hexamer
  • 2.56 MDa, 96 polymers
Theoretical massNumber of molelcules
Total (without water)2,564,64196
Polymers2,564,64196
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Major capsid protein


Mass: 45525.645 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Adjutor (virus) / References: UniProt: B2ZNR4
#2: Protein
gp_16 (Minor Capsid Protein)


Mass: 13766.352 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Adjutor (virus) / References: UniProt: B2ZNR3
#3: Protein HNH endonuclease


Mass: 6198.103 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Adjutor (virus) / References: UniProt: B2ZNQ1
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: Mycobacterium phage Adjutor / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacterium phage Adjutor (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Mycolicibacterium smegmatis MC2 155
Virus shellDiameter: 750 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTrisC4H11NO31
210 mMMagnesium sulfateMgSO41
368.44 mMSodium chlorideNaCl1
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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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: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 6664

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Processing

EM software
IDNameVersionCategoryDetails
4CTFFIND4.1CTF correctionFor initial estimation
5RELION3.1.0CTF correctionCTF Refinement
8Coot0.9.8.1model fitting
10PHENIX1.20.1model refinement
11ISOLDE1.3model refinement
12RELION3.1.0initial Euler assignment
13RELION3.1.0final Euler assignment
14RELION3.1.0classification
15RELION3.1.03D reconstruction
CTF correctionDetails: Standard CTF correction inside RELION's reconstruction.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44239 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Details: Amino acid sequence built into the map for a single major capsid protein and refined with Phenix. Model then used for rest of asymmetric unit and refined with Phenix. Final step involved using Isolde.

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