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- PDB-9ncf: Icosahedral capsid assembly of phage JohannRWettstein (Bas63) -

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Basic information

Entry
Database: PDB / ID: 9ncf
TitleIcosahedral capsid assembly of phage JohannRWettstein (Bas63)
Components
  • Head stabilization/decoration protein
  • Immunoglobulin-like domain protein
  • Major capsid protein
KeywordsVIRAL PROTEIN / Capsid / Major capsid protein / decoration protein / HOC-like / IG-like / phage / bacteriophage
Function / homology
Function and homology information


cell-cell adhesion / viral capsid / host cell cytoplasm / membrane
Similarity search - Function
Major capsid protein GpE / Phage major capsid protein E / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin-like domain protein / Head stabilization/decoration protein / Major capsid protein
Similarity search - Component
Biological speciesEscherichia phage JohannRWettstein (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsHodgkinson-Bean, J.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries (MAFF)GD0696J004 Japan
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
CitationJournal: To Be Published
Title: Icosahedral capsid assembly of phage JohannRWettstein (Bas63)
Authors: Hodgkinson-Bean, J. / Ayala, R. / McJarrow-Keller, K. / Cassin, L. / Rutter, G.L. / Crowe, A.J.M. / Wolf, M. / Bostina, M.
History
DepositionFeb 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: Head stabilization/decoration protein
K: Head stabilization/decoration protein
L: Head stabilization/decoration protein
M: Head stabilization/decoration protein
N: Head stabilization/decoration protein
O: Head stabilization/decoration protein
P: Head stabilization/decoration protein
Q: Head stabilization/decoration protein
R: Head stabilization/decoration protein
S: Immunoglobulin-like domain protein


Theoretical massNumber of molelcules
Total (without water)544,86119
Polymers544,86119
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: Head stabilization/decoration protein
K: Head stabilization/decoration protein
L: Head stabilization/decoration protein
M: Head stabilization/decoration protein
N: Head stabilization/decoration protein
O: Head stabilization/decoration protein
P: Head stabilization/decoration protein
Q: Head stabilization/decoration protein
R: Head stabilization/decoration protein
S: Immunoglobulin-like domain protein
x 60


Theoretical massNumber of molelcules
Total (without water)32,691,6861140
Polymers32,691,6861140
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
Major capsid protein / Major head protein


Mass: 41600.082 Da / Num. of mol.: 9 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE8B2A4
#2: Protein
Head stabilization/decoration protein


Mass: 13606.316 Da / Num. of mol.: 9 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE8B0J2
#3: Protein Immunoglobulin-like domain protein


Mass: 48003.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VUZ0
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: Escherichia phage JohannRWettstein / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 49.6 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30942 / Symmetry type: POINT

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