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- EMDB-44163: Pseudomonas phage Pa193 5-fold vertex (capsid, decorating, and sc... -

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Basic information

Entry
Database: EMDB / ID: EMD-44163
TitlePseudomonas phage Pa193 5-fold vertex (capsid, decorating, and scaffolding proteins)
Map data
Sample
  • Virus: Pseudomonas virus Pa193
    • Protein or peptide: gp26 Major capsid
    • Protein or peptide: gp25 Decorating protein
    • Protein or peptide: gp24 Scaffolding protein
Keywordsphage / bacteriophage / gene product 24 (gp24) / STRUCTURAL PROTEIN / VIRAL PROTEIN / gene product 25 (gp25) / scaffolding protein / decorating protein / major capsid protein / gene product 26 (gp26)
Function / homologyUncharacterised conserved protein UCP029215 / Uncharacterized protein conserved in bacteria (DUF2213) / : / Structural cement protein (E217 gp24/Pam3 gp6) / Virion protein / Capsid and scaffold protein / Capsid and scaffold protein
Function and homology information
Biological speciesPseudomonas virus Pa193
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsIglesias SM / Cingolani G
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44163.png

Downloads & links

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Map

FileDownload / File: emd_44163.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.34 Å/pix.
x 384 pix.
= 514.56 Å		1.34 Å/pix.
x 384 pix.
= 514.56 Å		1.34 Å/pix.
x 384 pix.
= 514.56 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-12.87707 - 27.436249
Average (Standard dev.)-0.00000000000102 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 514.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44163_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44163_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #1

Fileemd_44163_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Pseudomonas virus Pa193

EntireName: Pseudomonas virus Pa193
Components
  • Virus: Pseudomonas virus Pa193
    • Protein or peptide: gp26 Major capsid
    • Protein or peptide: gp25 Decorating protein
    • Protein or peptide: gp24 Scaffolding protein

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Supramolecule #1: Pseudomonas virus Pa193

SupramoleculeName: Pseudomonas virus Pa193 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2590837 / Sci species name: Pseudomonas virus Pa193 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: gp26 Major capsid

MacromoleculeName: gp26 Major capsid / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 41.610918 KDa
SequenceString: MSQISKTHSR LAGRNAKPFD LKNITNDAVA SLSRIGLVFD HAVVQDQIKA LAKAGAFRSG SAMDSNFTAP VTTPSIPTPI QFLQTWLPG FVKVMTAARK IDEIIGIDTV GSWEDQEIVQ GIVEPAGTAV EYGDHTNIPL TSWNANFERR TIVRGELGMM V GTLEEGRA ...String:
MSQISKTHSR LAGRNAKPFD LKNITNDAVA SLSRIGLVFD HAVVQDQIKA LAKAGAFRSG SAMDSNFTAP VTTPSIPTPI QFLQTWLPG FVKVMTAARK IDEIIGIDTV GSWEDQEIVQ GIVEPAGTAV EYGDHTNIPL TSWNANFERR TIVRGELGMM V GTLEEGRA SAIRLNSAET KRQQAAIGLE IFRNAIGFYG WQSGLGNRTY GFLNDPNLPA FQTPPSQGWS TADWAGIIGD IR EAVRQLR IQSQDQIDPK AEKITLALAT SKVDYLSVTT PYGISVSDWI EQTYPKMRIV SAPELSGVQM KAQEPEDALV LFV EDVNAA VDGSTDGGSV FSQLVQSKFI TLGVEKRAKS YVEDFSNGTA GALCKRPWAV VRYLGI

UniProtKB: Capsid and scaffold protein

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Macromolecule #2: gp25 Decorating protein

MacromoleculeName: gp25 Decorating protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 21.677443 KDa
SequenceString: MFQKQVYRQY TPGFPGDLIE DGPKRARPGR IMSLSAVNPA ATATGPNRIS RAFGYAGDVS ALGEGQPKTI AARASEVVIG GANFFGVLG HPKHYALFGS AGDSLAPSYD LPDGAEGEFF DMATGLVVEI FNGAATALDL DYGDLVAYVP NNLPTADNAL G LPAGALVG ...String:
MFQKQVYRQY TPGFPGDLIE DGPKRARPGR IMSLSAVNPA ATATGPNRIS RAFGYAGDVS ALGEGQPKTI AARASEVVIG GANFFGVLG HPKHYALFGS AGDSLAPSYD LPDGAEGEFF DMATGLVVEI FNGAATALDL DYGDLVAYVP NNLPTADNAL G LPAGALVG FKAGSMPTGL VQIPNARIVN AISLPAQSAG NLVAGVTIVQ LTQ

UniProtKB: Virion protein

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Macromolecule #3: gp24 Scaffolding protein

MacromoleculeName: gp24 Scaffolding protein / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 51.908012 KDa
SequenceString: MAKSKRKIDE NGYMTIEGCP ISSYGVFQYS AGQLGLPGDP MRIVNVYRPE SAVSDPEYIE SLKNLPLIDE HEMLSGFDDD DDSVAPEDK GVEGIITSNA YYEAPWARGD IRIYSRNMQN QLERGKEDLS LGYSCRYTEQ PGIWNGTPYE VVQDKMRGNH I ALVKEGRV ...String:
MAKSKRKIDE NGYMTIEGCP ISSYGVFQYS AGQLGLPGDP MRIVNVYRPE SAVSDPEYIE SLKNLPLIDE HEMLSGFDDD DDSVAPEDK GVEGIITSNA YYEAPWARGD IRIYSRNMQN QLERGKEDLS LGYSCRYTEQ PGIWNGTPYE VVQDKMRGNH I ALVKEGRV PGARVLDGLC FDHLSFDFRP SDEGNEMSLK KAKQKPPVQR VGQAADSAVE ELRALWPKLS ASVQKFLGEE AQ EPEHQEG AAAPAEPTDS EHMTEHPTLE GAQKDNEEHE EAPSVVDPAV AAAESERQES AASEMSGEGE VAELISQVKA ILA RLEGTA AEGADEEHGE GKDVVEGLEE QSSLSGSQTA SDDGGEGKDN SEELPEMAQK NAQDAAIRGL YRDIAAKDRL YKRL SSVVG AFDHRAMDSA EVAVYGVKKL NINCAKGQEA LALDMYLKGV EASRGAASRQ SKAQDSAGSA PQCAELDSYL KGE

UniProtKB: Capsid and scaffold protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 12520 / Average electron dose: 34.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.75 µm / Calibrated defocus min: 0.75 µm / Calibrated magnification: 64000 / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 46075
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 8278
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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