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- PDB-9b45: Pseudomonas phage Pa193 baseplate complex and tail fiber -

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Basic information

Entry
Database: PDB / ID: 9b45
TitlePseudomonas phage Pa193 baseplate complex and tail fiber
Components
  • gp34 helical bundle
  • gp35 Sheath initiator
  • gp37 Baseplate tube
  • gp38 Ripcord-1
  • gp39 Ripcord-2
  • gp41 Tape measure protein
  • gp42 Tail hub
  • gp44 Tail tip
  • gp45-a Baseplate wedge 1
  • gp46 Baseplate wedge 2
  • gp47 Tail fiber
KeywordsVIRAL PROTEIN / phage / bacteriophage / baseplate complex / STRUCTURAL PROTEIN / tail fiber
Function / homology
Function and homology information


peptidoglycan lytic transglycosylase activity / peptidoglycan metabolic process / membrane
Similarity search - Function
: / : / Baseplate hub gp41 / Baseplate component gp38 / Protein of unknown function DUF2612 / : / Protein of unknown function (DUF2612) / Tail fiber protein gp32 / Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain ...: / : / Baseplate hub gp41 / Baseplate component gp38 / Protein of unknown function DUF2612 / : / Protein of unknown function (DUF2612) / Tail fiber protein gp32 / Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain / Baseplate protein J-like / Baseplate J-like protein / Vgr protein, OB-fold domain superfamily / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Phage protein / Tail fiber protein / Tail fiber protein / Phage protein / Baseplate protein J-like domain-containing protein / Phage protein / Internal (Core) protein / Tail fiber protein / Phage protein / Baseplate protein
Similarity search - Component
Biological speciesPseudomonas virus Pa193
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsIglesias, S.M. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM140733 United States
CitationJournal: Commun Biol / Year: 2024
Title: Cryo-EM analysis of Pseudomonas phage Pa193 structural components.
Authors: Stephano M Iglesias / Chun-Feng David Hou / Johnny Reid / Evan Schauer / Renae Geier / Angela Soriaga / Lucy Sim / Lucy Gao / Julian Whitelegge / Pierre Kyme / Deborah Birx / Sebastien Lemire / Gino Cingolani /
Abstract: The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various ...The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various clinical settings, commonly called phage therapy, to address this growing public health crisis. Here, we describe a high-resolution structural atlas of a therapeutic, contractile-tailed Pseudomonas phage, Pa193. We used bioinformatics, proteomics, and cryogenic electron microscopy single particle analysis to identify, annotate, and build atomic models for 21 distinct structural polypeptide chains forming the icosahedral capsid, neck, contractile tail, and baseplate. We identified a putative scaffolding protein stabilizing the interior of the capsid 5-fold vertex. We also visualized a large portion of Pa193 ~ 500 Å long tail fibers and resolved the interface between the baseplate and tail fibers. The work presented here provides a framework to support a better understanding of phages as biomedicines for phage therapy and inform engineering opportunities.
History
DepositionMar 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
j: gp45-a Baseplate wedge 1
k: gp45-a Baseplate wedge 1
l: gp45-a Baseplate wedge 1
m: gp45-a Baseplate wedge 1
n: gp45-a Baseplate wedge 1
o: gp45-a Baseplate wedge 1
2: gp47 Tail fiber
3: gp47 Tail fiber
4: gp47 Tail fiber
A: gp34 helical bundle
B: gp34 helical bundle
C: gp34 helical bundle
D: gp34 helical bundle
E: gp34 helical bundle
F: gp34 helical bundle
S: gp38 Ripcord-1
T: gp38 Ripcord-1
U: gp38 Ripcord-1
a: gp41 Tape measure protein
b: gp41 Tape measure protein
c: gp41 Tape measure protein
d: gp42 Tail hub
e: gp42 Tail hub
f: gp42 Tail hub
V: gp39 Ripcord-2
W: gp39 Ripcord-2
X: gp39 Ripcord-2
v: gp46 Baseplate wedge 2
w: gp46 Baseplate wedge 2
x: gp46 Baseplate wedge 2
y: gp46 Baseplate wedge 2
z: gp46 Baseplate wedge 2
1: gp46 Baseplate wedge 2
q: gp45-a Baseplate wedge 1
p: gp45-a Baseplate wedge 1
r: gp45-a Baseplate wedge 1
s: gp45-a Baseplate wedge 1
t: gp45-a Baseplate wedge 1
u: gp45-a Baseplate wedge 1
M: gp37 Baseplate tube
N: gp37 Baseplate tube
O: gp37 Baseplate tube
P: gp37 Baseplate tube
Q: gp37 Baseplate tube
R: gp37 Baseplate tube
G: gp35 Sheath initiator
H: gp35 Sheath initiator
I: gp35 Sheath initiator
J: gp35 Sheath initiator
K: gp35 Sheath initiator
L: gp35 Sheath initiator
g: gp44 Tail tip
h: gp44 Tail tip
i: gp44 Tail tip


Theoretical massNumber of molelcules
Total (without water)1,989,48554
Polymers1,989,48554
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 11 types, 54 molecules jklmnoqprstu234ABCDEFSTUabcdef...

#1: Protein
gp45-a Baseplate wedge 1


Mass: 43189.418 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KVA6
#2: Protein gp47 Tail fiber


Mass: 103353.273 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KV60
#3: Protein
gp34 helical bundle


Mass: 12270.898 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5Q5ANU9
#4: Protein gp38 Ripcord-1


Mass: 20000.949 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193
#5: Protein gp41 Tape measure protein


Mass: 94380.547 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KVB9
#6: Protein gp42 Tail hub


Mass: 32480.277 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KVA7
#7: Protein gp39 Ripcord-2


Mass: 21667.574 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KV96
#8: Protein
gp46 Baseplate wedge 2


Mass: 54629.078 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KVD4
#9: Protein
gp37 Baseplate tube


Mass: 17748.182 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KV51
#10: Protein
gp35 Sheath initiator


Mass: 12511.949 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KV99
#11: Protein gp44 Tail tip


Mass: 24201.186 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5Q5ANV0

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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: Pseudomonas virus Pa193 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudomonas virus Pa193
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Pseudomonas aeruginosa
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 64000 X / Calibrated magnification: 64000 X / Nominal defocus max: 1750 nm / Nominal defocus min: 750 nm / Calibrated defocus min: 750 nm / Calibrated defocus max: 1750 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 34.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 12520

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
4RELION4CTF correction
9RELION4initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
13PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 40335
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17175 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007106395
ELECTRON MICROSCOPYf_angle_d0.858145023
ELECTRON MICROSCOPYf_dihedral_angle_d5.38214853
ELECTRON MICROSCOPYf_chiral_restr0.04816659
ELECTRON MICROSCOPYf_plane_restr0.00819035

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