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- PDB-9ndy: Composite baseplate asymmetric unit of JohannRWettstein (Bas63) -

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Basic information

Entry
Database: PDB / ID: 9ndy
TitleComposite baseplate asymmetric unit of JohannRWettstein (Bas63)
Components
  • (Wedge protein ...) x 2
  • Hub protein (gp020)
  • LTF platform protein (gp025)
  • Puncture apparatus (gp021)
  • Sheath initiator (gp022)
  • Spacer protein (gp019)
  • Tape measure protein (gp017)
  • Tube initiator protein (gp018)
KeywordsVIRAL PROTEIN / baseplate / wedge / hub / puncture apparatus / sheath initiator / tube initiator / tape measure protein / LTF-platform / spacer / phage / bacteriophage
Function / homology
Function and homology information


viral tail assembly
Similarity search - Function
: / Dit-like phage tail protein / : / Cyanophage baseplate Pam3 plug gp18 / Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain / Tape measure protein N-terminal / Tape measure protein / Baseplate protein J-like / Baseplate J-like protein barrel domain / Vgr protein, OB-fold domain superfamily
Similarity search - Domain/homology
Cyanophage baseplate Pam3 plug gp18 domain-containing protein / Tail length tape-measure protein / Dit-like phage tail protein N-terminal domain-containing protein / Phage protein / Baseplate wedge subunit / Baseplate protein / Baseplate protein / Baseplate assembly protein / Phage protein
Similarity search - Component
Biological speciesEscherichia phage JohannRWettstein (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 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 18, 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: 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: Tube initiator protein (gp018)
B: Tube initiator protein (gp018)
C: Sheath initiator (gp022)
D: Sheath initiator (gp022)
E: Hub protein (gp020)
F: Tape measure protein (gp017)
G: Puncture apparatus (gp021)
H: Wedge protein 2 (gp023)
I: Wedge protein 2 (gp023)
J: Wedge protein 1 (gp024)
K: Wedge protein 2 (gp023)
L: Wedge protein 2 (gp023)
M: Wedge protein 1 (gp024)
N: Spacer protein (gp019)
O: Spacer protein (gp019)
S: LTF platform protein (gp025)
T: LTF platform protein (gp025)
U: LTF platform protein (gp025)
P: LTF platform protein (gp025)
Q: LTF platform protein (gp025)
R: LTF platform protein (gp025)


Theoretical massNumber of molelcules
Total (without water)597,97021
Polymers597,97021
Non-polymers00
Water00
1
A: Tube initiator protein (gp018)
B: Tube initiator protein (gp018)
C: Sheath initiator (gp022)
D: Sheath initiator (gp022)
E: Hub protein (gp020)
F: Tape measure protein (gp017)
G: Puncture apparatus (gp021)
H: Wedge protein 2 (gp023)
I: Wedge protein 2 (gp023)
J: Wedge protein 1 (gp024)
K: Wedge protein 2 (gp023)
L: Wedge protein 2 (gp023)
M: Wedge protein 1 (gp024)
N: Spacer protein (gp019)
O: Spacer protein (gp019)
S: LTF platform protein (gp025)
T: LTF platform protein (gp025)
U: LTF platform protein (gp025)
P: LTF platform protein (gp025)
Q: LTF platform protein (gp025)
R: LTF platform protein (gp025)

A: Tube initiator protein (gp018)
B: Tube initiator protein (gp018)
C: Sheath initiator (gp022)
D: Sheath initiator (gp022)
E: Hub protein (gp020)
F: Tape measure protein (gp017)
G: Puncture apparatus (gp021)
H: Wedge protein 2 (gp023)
I: Wedge protein 2 (gp023)
J: Wedge protein 1 (gp024)
K: Wedge protein 2 (gp023)
L: Wedge protein 2 (gp023)
M: Wedge protein 1 (gp024)
N: Spacer protein (gp019)
O: Spacer protein (gp019)
S: LTF platform protein (gp025)
T: LTF platform protein (gp025)
U: LTF platform protein (gp025)
P: LTF platform protein (gp025)
Q: LTF platform protein (gp025)
R: LTF platform protein (gp025)

A: Tube initiator protein (gp018)
B: Tube initiator protein (gp018)
C: Sheath initiator (gp022)
D: Sheath initiator (gp022)
E: Hub protein (gp020)
F: Tape measure protein (gp017)
G: Puncture apparatus (gp021)
H: Wedge protein 2 (gp023)
I: Wedge protein 2 (gp023)
J: Wedge protein 1 (gp024)
K: Wedge protein 2 (gp023)
L: Wedge protein 2 (gp023)
M: Wedge protein 1 (gp024)
N: Spacer protein (gp019)
O: Spacer protein (gp019)
S: LTF platform protein (gp025)
T: LTF platform protein (gp025)
U: LTF platform protein (gp025)
P: LTF platform protein (gp025)
Q: LTF platform protein (gp025)
R: LTF platform protein (gp025)


Theoretical massNumber of molelcules
Total (without water)1,793,91063
Polymers1,793,91063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2

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Components

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Protein , 7 types, 15 molecules ABCDEFGNOSTUPQR

#1: Protein Tube initiator protein (gp018)


Mass: 28593.939 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VVH7
#2: Protein Sheath initiator (gp022)


Mass: 15632.561 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE8B0J9
#3: Protein Hub protein (gp020)


Mass: 37204.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VWE1
#4: Protein Tape measure protein (gp017)


Mass: 80340.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VV46
#5: Protein Puncture apparatus (gp021)


Mass: 23186.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE8B143
#8: Protein Spacer protein (gp019)


Mass: 13209.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VUR9
#9: Protein
LTF platform protein (gp025)


Mass: 11093.398 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE8B758

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Wedge protein ... , 2 types, 6 molecules HIKLJM

#6: Protein
Wedge protein 2 (gp023)


Mass: 53139.953 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE8B2A9
#7: Protein Wedge protein 1 (gp024)


Mass: 31622.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE8B2H1

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Details

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: #3, #9, #8, #4, #6 / 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 software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14390
Details: The final reconstruction is a composite reconstruction of maps under accessions:EMD-49262, EMD-49264 and EMD-49265. Particle number and resolution are reported from the consensus reconstruction used (EMD-49262).
Symmetry type: POINT

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