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- PDB-8eb4: Gordonia phage Ziko -

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Basic information

Entry
Database: PDB / ID: 8eb4
TitleGordonia phage Ziko
ComponentsMajor capsid protein
KeywordsVIRUS / HK97-fold / T=9 / tailed bacteriophage
Function / homologyPhage capsid / Phage capsid family / Major capsid protein
Function and homology information
Biological speciesGordonia phage Ziko (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsPodgorski, J.M. / White, S.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2023
Title: A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability.
Authors: Jennifer M Podgorski / Krista Freeman / Sophia Gosselin / Alexis Huet / James F Conway / Mary Bird / John Grecco / Shreya Patel / Deborah Jacobs-Sera / Graham Hatfull / Johann Peter Gogarten ...Authors: Jennifer M Podgorski / Krista Freeman / Sophia Gosselin / Alexis Huet / James F Conway / Mary Bird / John Grecco / Shreya Patel / Deborah Jacobs-Sera / Graham Hatfull / Johann Peter Gogarten / Janne Ravantti / Simon J White /
Abstract: Many double-stranded DNA viruses, including tailed bacteriophages (phages) and herpesviruses, use the HK97-fold in their major capsid protein to make the capsomers of the icosahedral viral capsid. ...Many double-stranded DNA viruses, including tailed bacteriophages (phages) and herpesviruses, use the HK97-fold in their major capsid protein to make the capsomers of the icosahedral viral capsid. After the genome packaging at near-crystalline densities, the capsid is subjected to a major expansion and stabilization step that allows it to withstand environmental stresses and internal high pressure. Several different mechanisms for stabilizing the capsid have been structurally characterized, but how these mechanisms have evolved is still not understood. Using cryo-EM structure determination of 10 capsids, structural comparisons, phylogenetic analyses, and Alphafold predictions, we have constructed a detailed structural dendrogram describing the evolution of capsid structural stability within the actinobacteriophages. We show that the actinobacteriophage major capsid proteins can be classified into 15 groups based upon their HK97-fold.
History
DepositionAug 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
F: Major capsid protein
E: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
I: Major capsid protein
H: Major capsid protein
G: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)307,8289
Polymers307,8289
Non-polymers00
Water00
1
A: Major capsid protein
F: Major capsid protein
E: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
I: Major capsid protein
H: Major capsid protein
G: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)18,469,690540
Polymers18,469,690540
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
F: Major capsid protein
E: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
I: Major capsid protein
H: Major capsid protein
G: Major capsid protein
x 5


  • icosahedral pentamer
  • 1.54 MDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)1,539,14145
Polymers1,539,14145
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
F: Major capsid protein
E: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
I: Major capsid protein
H: Major capsid protein
G: Major capsid protein
x 6


  • icosahedral 23 hexamer
  • 1.85 MDa, 54 polymers
Theoretical massNumber of molelcules
Total (without water)1,846,96954
Polymers1,846,96954
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 / gp42


Mass: 34203.129 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Gordonia phage Ziko (virus) / References: UniProt: A0A514A559

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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: Gordonia phage Ziko / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Gordonia phage Ziko (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Gordonia terrae
Virus shellDiameter: 760 nm / Triangulation number (T number): 9
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: 0.87 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5058

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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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35950 / 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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