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- PDB-8edu: Mycobacteriophage Muddy capsid -

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Basic information

Entry
Database: PDB / ID: 8edu
TitleMycobacteriophage Muddy capsid
ComponentsCapsid
KeywordsVIRUS / Bacteriophage / Mycobacteriophage / HK97-fold / Capsid
Function / homologyPhage capsid / Phage capsid family / Capsid protein
Function and homology information
Biological speciesMycobacterium phage Muddy (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFreeman, K.G. / White, S.J. / Huet, A. / Conway, J.F.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131729 United States
Howard Hughes Medical Institute (HHMI)GT12053 United States
National Institutes of Health/Office of the DirectorOD019995 United States
National Institutes of Health/Office of the DirectorOD025009 United States
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
DepositionSep 6, 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: Capsid
G: Capsid
D: Capsid
F: Capsid
B: Capsid
E: Capsid
C: Capsid


Theoretical massNumber of molelcules
Total (without water)242,6917
Polymers242,6917
Non-polymers00
Water00
1
A: Capsid
G: Capsid
D: Capsid
F: Capsid
B: Capsid
E: Capsid
C: Capsid
x 60


Theoretical massNumber of molelcules
Total (without water)14,561,443420
Polymers14,561,443420
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: Capsid
G: Capsid
D: Capsid
F: Capsid
B: Capsid
E: Capsid
C: Capsid
x 5


  • icosahedral pentamer
  • 1.21 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,213,45435
Polymers1,213,45435
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid
G: Capsid
D: Capsid
F: Capsid
B: Capsid
E: Capsid
C: Capsid
x 6


  • icosahedral 23 hexamer
  • 1.46 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,456,14442
Polymers1,456,14442
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
Capsid / gp9


Mass: 34670.102 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Muddy (virus) / References: UniProt: S5Y5B1

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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 Muddy / Type: VIRUS
Details: Phage Muddy particles generated by amplification on bacterial host and purification via CsCl gradient.
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacterium phage Muddy (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Mycolicibacterium smegmatis MC2 155
Virus shellDiameter: 710 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTrisC4H11NO31
21 mMMagnesium sulfateMgSO41
368.44 mMSodium chlorideNaCl1
41 mMCalcium chlorideCaCl21
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / 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 magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 40 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1027
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails
2EPU2.11image acquisition
4CTFFIND4.1CTF correctionFor initial estimation
5RELION3.1.1CTF correctionCTF Refinement
8Coot0.9.4.1model fitting
10RELION3.1.1initial Euler assignment
11RELION3.1.1final Euler assignment
12RELION3.1.1classification
13RELION3.1.13D reconstruction
14PHENIX1.19.2model refinement
15ISOLDE1.3model refinement
CTF correctionDetails: Standard CTF correction inside RELION's reconstruction.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 28207
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25244 / 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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