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- PDB-9d82: Shigella flexneri bacteriophage B2 Icosahedral Reconstruction -

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Basic information

Entry
Database: PDB / ID: 9d82
TitleShigella flexneri bacteriophage B2 Icosahedral Reconstruction
Components
  • B2 Capsid
  • B2 Dec Gp45
KeywordsVIRUS / B2
Biological speciesShigella phage B2 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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: B2 Capsid
B: B2 Capsid
C: B2 Capsid
D: B2 Capsid
E: B2 Capsid
F: B2 Capsid
G: B2 Capsid
H: B2 Capsid
I: B2 Capsid
J: B2 Dec Gp45
K: B2 Dec Gp45
L: B2 Dec Gp45
M: B2 Dec Gp45
N: B2 Dec Gp45
O: B2 Dec Gp45
P: B2 Dec Gp45
Q: B2 Dec Gp45
R: B2 Dec Gp45


Theoretical massNumber of molelcules
Total (without water)468,23518
Polymers468,23518
Non-polymers00
Water00
1
A: B2 Capsid
B: B2 Capsid
C: B2 Capsid
D: B2 Capsid
E: B2 Capsid
F: B2 Capsid
G: B2 Capsid
H: B2 Capsid
I: B2 Capsid
J: B2 Dec Gp45
K: B2 Dec Gp45
L: B2 Dec Gp45
M: B2 Dec Gp45
N: B2 Dec Gp45
O: B2 Dec Gp45
P: B2 Dec Gp45
Q: B2 Dec Gp45
R: B2 Dec Gp45
x 60


Theoretical massNumber of molelcules
Total (without water)28,094,1101080
Polymers28,094,1101080
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
B2 Capsid


Mass: 42530.359 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage B2 (virus) / Production host: Shigella flexneri 2a str. 2457T (bacteria)
#2: Protein
B2 Dec Gp45


Mass: 9495.771 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage B2 (virus) / Production host: Shigella flexneri 2a str. 2457T (bacteria)
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 phage B2 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Shigella phage B2 (virus)
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: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135384 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00328738
ELECTRON MICROSCOPYf_angle_d0.69739032
ELECTRON MICROSCOPYf_dihedral_angle_d4.5664029
ELECTRON MICROSCOPYf_chiral_restr0.0424493
ELECTRON MICROSCOPYf_plane_restr0.0055022

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