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- PDB-9gb2: Extended phiCD508 baseplate -

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Basic information

Entry
Database: PDB / ID: 9gb2
TitleExtended phiCD508 baseplate
Components
  • gp55 - Tail sheath protein
  • gp56 - Tail tube protein
  • gp61 - Tail tube initiator
  • gp64 - Sheath initiator
  • gp65 - Triplex 1a protein
  • gp66 - Triplex 2 protein
KeywordsVIRUS / Bacteriophage / needle / baseplate
Function / homology
Function and homology information


Bacteriophage Mu-like, Gp48 / : / Bacteriophage Mu-like, Gp48 / : / Protein of unknown function DUF2634 / Protein of unknown function (DUF2634) / Phage tail tube protein / XkdM-like superfamily / Phage tail tube protein / Phage tail sheath protein, beta-sandwich domain ...Bacteriophage Mu-like, Gp48 / : / Bacteriophage Mu-like, Gp48 / : / Protein of unknown function DUF2634 / Protein of unknown function (DUF2634) / Phage tail tube protein / XkdM-like superfamily / Phage tail tube protein / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Baseplate protein J-like / Baseplate J-like protein / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
LysM domain/BON superfamily protein / Protein of uncharacterized function (DUF2001) / Phage tail sheath protein / XkdT-related protein / Baseplate J family protein / XkdS-related protein
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsWilson, J.S. / Fagan, R.P. / Bullough, P.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P02002X/1 United Kingdom
CitationJournal: Life Sci Alliance / Year: 2025
Title: Molecular mechanism of bacteriophage contraction structure of an S-layer-penetrating bacteriophage.
Authors: Jason S Wilson / Louis-Charles Fortier / Robert P Fagan / Per A Bullough /
Abstract: The molecular details of phage tail contraction and bacterial cell envelope penetration remain poorly understood and are completely unknown for phages infecting bacteria enveloped by proteinaceous S- ...The molecular details of phage tail contraction and bacterial cell envelope penetration remain poorly understood and are completely unknown for phages infecting bacteria enveloped by proteinaceous S-layers. Here, we reveal the extended and contracted atomic structures of an intact contractile-tailed phage (φCD508) that binds to and penetrates the protective S-layer of the Gram-positive human pathogen The tail is unusually long (225 nm), and it is also notable that the tail contracts less than those studied in related contractile injection systems such as the model phage T4 (∼20% compared with ∼50%). Surprisingly, we find no evidence of auxiliary enzymatic domains that other phages exploit in cell wall penetration, suggesting that sufficient energy is released upon tail contraction to penetrate the S-layer and the thick cell wall without enzymatic activity. Instead, the unusually long tail length, which becomes more flexible upon contraction, likely contributes toward the required free energy release for envelope penetration.
History
DepositionJul 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: gp65 - Triplex 1a protein
B: gp65 - Triplex 1a protein
C: gp65 - Triplex 1a protein
D: gp65 - Triplex 1a protein
E: gp65 - Triplex 1a protein
F: gp65 - Triplex 1a protein
G: gp65 - Triplex 1a protein
H: gp65 - Triplex 1a protein
I: gp65 - Triplex 1a protein
J: gp65 - Triplex 1a protein
K: gp65 - Triplex 1a protein
L: gp65 - Triplex 1a protein
M: gp66 - Triplex 2 protein
N: gp66 - Triplex 2 protein
O: gp66 - Triplex 2 protein
P: gp66 - Triplex 2 protein
Q: gp66 - Triplex 2 protein
R: gp66 - Triplex 2 protein
S: gp61 - Tail tube initiator
T: gp61 - Tail tube initiator
U: gp61 - Tail tube initiator
V: gp61 - Tail tube initiator
W: gp61 - Tail tube initiator
X: gp61 - Tail tube initiator
Y: gp56 - Tail tube protein
Z: gp56 - Tail tube protein
a: gp56 - Tail tube protein
b: gp56 - Tail tube protein
c: gp56 - Tail tube protein
d: gp56 - Tail tube protein
e: gp55 - Tail sheath protein
f: gp55 - Tail sheath protein
g: gp55 - Tail sheath protein
h: gp55 - Tail sheath protein
i: gp55 - Tail sheath protein
j: gp55 - Tail sheath protein
k: gp64 - Sheath initiator
l: gp64 - Sheath initiator
m: gp64 - Sheath initiator
n: gp64 - Sheath initiator
o: gp64 - Sheath initiator
p: gp64 - Sheath initiator


Theoretical massNumber of molelcules
Total (without water)1,314,50242
Polymers1,314,50242
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 6 types, 42 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#1: Protein
gp65 - Triplex 1a protein


Mass: 41502.496 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Strain: CD117 / References: UniProt: J9QE72
#2: Protein
gp66 - Triplex 2 protein


Mass: 23912.678 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Strain: CD117 / References: UniProt: J9QE20
#3: Protein
gp61 - Tail tube initiator


Mass: 25899.830 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Strain: CD117 / References: UniProt: A0A9X8RMX4
#4: Protein
gp56 - Tail tube protein


Mass: 15572.538 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Strain: CD117 / References: UniProt: A0A9X8RMX9
#5: Protein
gp55 - Tail sheath protein


Mass: 53016.762 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Strain: CD117 / References: UniProt: A0A9X8RMY4
#6: Protein
gp64 - Sheath initiator


Mass: 17676.939 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Strain: CD117 / References: UniProt: J9QEB8

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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: Extended phiCD508 baseplate / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19276 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 202.69 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025174678
ELECTRON MICROSCOPYf_angle_d0.6699316854
ELECTRON MICROSCOPYf_chiral_restr0.044913716
ELECTRON MICROSCOPYf_plane_restr0.002425800
ELECTRON MICROSCOPYf_dihedral_angle_d10.94827558

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