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- EMDB-44164: Pseudomonas phage Pa193 Neck (portal and head-to-tail proteins) -

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Basic information

Entry
Database: EMDB / ID: EMD-44164
TitlePseudomonas phage Pa193 Neck (portal and head-to-tail proteins)
Map data
Sample
  • Virus: Pseudomonas virus Pa193
    • Protein or peptide: gp19 Portal
    • Protein or peptide: gp28 Head-to-tail protein
Keywordsphage / bacteriophage / gene product (gp19) / STRUCTURAL PROTEIN / VIRAL PROTEIN / gene product 28 (gp28) / head-to-tail protein / portal protein
Function / homologyProtein of unknown function DUF4054 / Inorganic pyrophosphatase domain / Protein of unknown function (DUF4054) / Inorganic Pyrophosphatase / Protein of unknown function DUF1073 / Anti-CBASS protein Acb1-like / Phage protein / Inorganic pyrophosphatase domain-containing protein
Function and homology information
Biological speciesPseudomonas virus Pa193
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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_44164.png

Downloads & links

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Map

FileDownload / File: emd_44164.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesX (Sec.)Y (Row.)Z (Col.)
1.34 Å/pix.
x 320 pix.
= 428.8 Å		1.34 Å/pix.
x 320 pix.
= 428.8 Å		1.34 Å/pix.
x 320 pix.
= 428.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-17.129093000000001 - 32.688557000000003
Average (Standard dev.)0.000000000005013 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 428.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44164_msk_1.map
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Additional map: #1

Fileemd_44164_additional_1.map
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Half map: #2

Fileemd_44164_half_map_1.map
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Half map: #1

Fileemd_44164_half_map_2.map
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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: gp19 Portal
    • Protein or peptide: gp28 Head-to-tail 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

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Macromolecule #1: gp19 Portal

MacromoleculeName: gp19 Portal / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 84.4785 KDa
SequenceString: MFKLSWIFGR KKDNAACSES APEKVAQIPQ HDPLDPMIKL GRIRGWNVEP EKAPVIRSVK DFLEPGLSVA MDSAYGDGPT PAAKAAAGG QNPYVVPTML QDWYNSQGFI GYQACAIISQ HWLVDKACSM SGEDAARNGW ELKSDGRKLS DEQSALIARR D MEFRVKDN ...String:
MFKLSWIFGR KKDNAACSES APEKVAQIPQ HDPLDPMIKL GRIRGWNVEP EKAPVIRSVK DFLEPGLSVA MDSAYGDGPT PAAKAAAGG QNPYVVPTML QDWYNSQGFI GYQACAIISQ HWLVDKACSM SGEDAARNGW ELKSDGRKLS DEQSALIARR D MEFRVKDN LVELNRFKNV FGVRIALFVV ESDDPDYYEK PFNPDGITPG SYKGISQIDP YWAMPQLTAG STADPSSEHF YE PDFWIIS GKKYHRSHLV VVRGPQPPDI LKPTYIFGGI PLTQRIYERV YAAERTANEA PLLAMSKRTS TIHVDVEKAI ANE DAFNAR LAFWIANRDN HGVKVLGTDE SMEQFDTNLA DFDSIIMNQY QLVAAIAKTP ATKLLGTSPK GFNATGEHET ISYH EELES IQEHIFDPLL ERHYLLLAKS EEIDVQLEIV WNPVDSTSSQ QQAELNNKKA ATDEIYINSG VVSPDEVRER LRDDP RSGY NRLTDDQAET EPGMSPENLA EFEKAGAQSA KAKGEAERAE AQAGAVEGAG DPVPAAPRGT KPLAKAAEEG ASEAAE PPS RPDPKAELRN LLVDLLSKLQ DLDDIKAPDG VDIEHNDAPG VKRTSKPGVS GMEPSVFSSN RIVGPRDHSE LQRIKVN GI TTLIENPRGS IRQGKDGSWR VQMKHHYGFI KGTKGADGDE VDCFVGPNLG SKRVFVVNQV NKEGQFDEHK CMLGFNNI N DAKSGYLSCF RPGWDGLGSI HEVDLPAFRR WLANGDTTKP FGGE

UniProtKB: Inorganic pyrophosphatase domain-containing protein

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Macromolecule #2: gp28 Head-to-tail protein

MacromoleculeName: gp28 Head-to-tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 16.885285 KDa
SequenceString:
MVIFDEHKFR TLFPEFADPA AYPDVRLQMY FDIACEFISD RDSPYRILNG KALEACLYLL TAHLLSLSTM QVQGAAGGGV TAGGTQGGF ITSATVGEVS VAKLAPPAKN GWQWWLSGTP YGQELWALLS VKAVGGFYIG GLPERRGFRK VGGTFW

UniProtKB: Phage 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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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: C12 (12 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 9179
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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