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- PDB-8fvh: Pseudomonas phage E217 neck (portal, head-to-tail connector, coll... -

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Basic information

Entry
Database: PDB / ID: 8fvh
TitlePseudomonas phage E217 neck (portal, head-to-tail connector, collar and gateway proteins)
Components
  • E217 collar protein gp28
  • E217 gateway protein gp29
  • E217 head-to-tail connector protein gp27
  • E217 portal protein gp19
KeywordsVIRUS / pseudomonas / phage / E217
Function / homology
Function and homology information


Inorganic pyrophosphatase domain / : / : / Inorganic Pyrophosphatase / E217 collar protein gp28 / E217 gateway protein gp29 / Protein of unknown function DUF4054 / Protein of unknown function (DUF4054) / Protein of unknown function DUF1073 / Phage portal protein
Similarity search - Domain/homology
Phage protein / Uncharacterized protein / Phage protein / Virion protein
Similarity search - Component
Biological speciesPseudomonas phage vB_PaeM_E217 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLi, F. / Cingolani, G. / Hou, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM140733 United States
CitationJournal: Nat Commun / Year: 2023
Title: High-resolution cryo-EM structure of the Pseudomonas bacteriophage E217.
Authors: Fenglin Li / Chun-Feng David Hou / Ravi K Lokareddy / Ruoyu Yang / Francesca Forti / Federica Briani / Gino Cingolani /
Abstract: E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after ...E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after DNA ejection at 3.1 Å and 4.5 Å resolution, respectively, determined using cryogenic electron microscopy (cryo-EM). We identify and build de novo structures for 19 unique E217 gene products, resolve the tail genome-ejection machine in both extended and contracted states, and decipher the complete architecture of the baseplate formed by 66 polypeptide chains. We also determine that E217 recognizes the host O-antigen as a receptor, and we resolve the N-terminal portion of the O-antigen-binding tail fiber. We propose that E217 design principles presented in this paper are conserved across PB1-like Myoviridae phages of the Pbunavirus genus that encode a ~1.4 MDa baseplate, dramatically smaller than the coliphage T4.
History
DepositionJan 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 14, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: E217 collar protein gp28
A: E217 collar protein gp28
B: E217 collar protein gp28
D: E217 collar protein gp28
E: E217 collar protein gp28
F: E217 collar protein gp28
M: E217 gateway protein gp29
P: E217 gateway protein gp29
S: E217 gateway protein gp29
V: E217 gateway protein gp29
Y: E217 gateway protein gp29
b: E217 gateway protein gp29
N: E217 head-to-tail connector protein gp27
Q: E217 head-to-tail connector protein gp27
T: E217 head-to-tail connector protein gp27
W: E217 head-to-tail connector protein gp27
Z: E217 head-to-tail connector protein gp27
c: E217 head-to-tail connector protein gp27
G: E217 head-to-tail connector protein gp27
H: E217 head-to-tail connector protein gp27
I: E217 head-to-tail connector protein gp27
J: E217 head-to-tail connector protein gp27
K: E217 head-to-tail connector protein gp27
L: E217 head-to-tail connector protein gp27
O: E217 portal protein gp19
R: E217 portal protein gp19
U: E217 portal protein gp19
X: E217 portal protein gp19
a: E217 portal protein gp19
d: E217 portal protein gp19
e: E217 portal protein gp19
f: E217 portal protein gp19
g: E217 portal protein gp19
h: E217 portal protein gp19
i: E217 portal protein gp19
j: E217 portal protein gp19


Theoretical massNumber of molelcules
Total (without water)998,00536
Polymers998,00536
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
E217 collar protein gp28


Mass: 14234.122 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8I4A6
#2: Protein
E217 gateway protein gp29


Mass: 21057.492 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HWZ4
#3: Protein
E217 head-to-tail connector protein gp27


Mass: 16885.285 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HNR2
#4: Protein
E217 portal protein gp19


Mass: 48635.984 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HWX3
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: Pseudomonas phage vB_PaeM_E217 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 8
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: OTHER
Electron lensMode: OTHER / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2RELION3.1.2image acquisition
4RELION3.1.2CTF correction
8PHENIXmodel refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9300
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00372114
ELECTRON MICROSCOPYf_angle_d0.55997848
ELECTRON MICROSCOPYf_dihedral_angle_d4.6059660
ELECTRON MICROSCOPYf_chiral_restr0.04310404
ELECTRON MICROSCOPYf_plane_restr0.00412912

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