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- PDB-9d7z: Shigella flexneri bacteriophage Moo19 Icosahedral Reconstruction -

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Basic information

Entry
Database: PDB / ID: 9d7z
TitleShigella flexneri bacteriophage Moo19 Icosahedral Reconstruction
Components
  • Ig-like domain-containing protein
  • Major capsid protein
KeywordsVIRUS / Moo19
Function / homologyPhage capsid protein / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Ig-like domain-containing protein / Major capsid protein
Function and homology information
Biological speciesShigella virus Moo19
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSubramanian, S. / Bergland Drarvik, S.M. / Parent, K.N.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140803 United States
National Science Foundation (NSF, United States)1750125 United States
CitationJournal: Sci Adv / Year: 2024
Title: Moo19 and B2: Structures of podophages with = 9 geometry and tailspikes with esterase activity.
Authors: Sundharraman Subramanian / Silje M Bergland Drarvik / Kendal R Tinney / Sarah M Doore / Kristin N Parent /
Abstract: Podophages are, by far, the least well studied of all the bacteriophages. Despite being classified together due to their short, noncontractile tails, there is a huge amount of diversity among members ...Podophages are, by far, the least well studied of all the bacteriophages. Despite being classified together due to their short, noncontractile tails, there is a huge amount of diversity among members of this group. Of the podophages, the N4-like family is the least well studied structurally and is quite divergent from well-characterized podophages such as T7 and P22. In this work, we isolate and fully characterize two members of the family by cryo-electron microscopy, genetics, and biochemistry. We describe the capsid features of Moo19 and B2, including a decoration protein. In addition, we have fully modeled the tail machinery for both phages and identify proteins with esterase activity. Genetic knockouts of the host reveal factors specific for host attachment including key modifications to the O-antigen on the lipopolysaccharide. Moo19 and B2 are both members, yet some distinct differences in the genome and structure place them into distinct clades.
History
DepositionAug 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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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
H: Major capsid protein
I: Major capsid protein
J: Ig-like domain-containing protein
K: Ig-like domain-containing protein
L: Ig-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)480,14612
Polymers480,14612
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
H: Major capsid protein
I: Major capsid protein
J: Ig-like domain-containing protein
K: Ig-like domain-containing protein
L: Ig-like domain-containing protein
x 60


Theoretical massNumber of molelcules
Total (without water)28,808,771720
Polymers28,808,771720
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
Major capsid protein


Mass: 43971.672 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella virus Moo19 / Gene: Moo19_gp73 / Production host: Shigella flexneri 2a str. 2457T (bacteria) / References: UniProt: A0AAE8YCM0
#2: Protein Ig-like domain-containing protein


Mass: 28133.709 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella virus Moo19 / Gene: Moo19_gp28 / Production host: Shigella flexneri 2a str. 2457T (bacteria) / References: UniProt: A0AAE8YCJ7
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: Shigella virus Moo19 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Shigella virus Moo19
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Shigella flexneri 2a str. 2457T
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMtris(hydroxymethyl)aminomethane1
210 mMmagnesium chlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 33 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFINDCTF correction
10RELION4.0.1initial Euler assignment
11RELION4.0.1final Euler assignment
13RELION4.0.13D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99582 / Symmetry type: POINT

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