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- EMDB-44166: Pseudomonas phage Pa193 neck and extended tail (collar, gateway, ... -

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Basic information

Entry
Database: EMDB / ID: EMD-44166
TitlePseudomonas phage Pa193 neck and extended tail (collar, gateway, tail tube, and sheath proteins)
Map data
Sample
  • Virus: Pseudomonas virus Pa193
    • Protein or peptide: gp32 Sheath
    • Protein or peptide: gp29 Collar
    • Protein or peptide: gp33 Tail tube
    • Protein or peptide: gp30 Gateway
Keywordsphage / bacteriophage / gene product (gp29) / STRUCTURAL PROTEIN / VIRAL PROTEIN / gene product 30 (gp30) / collar protein / gateway protein / sheath protein / tail tube protein / gene product 32 (gp32) / gene product 33 (gp33)
Function / homology
Function and homology information


: / : / E217 collar protein gp28 / E217 gateway protein gp29 / : / Tail fiber protein gp32 / Protein of unknown function DUF3383 / Protein of unknown function (DUF3383)
Similarity search - Domain/homology
Virion protein / Tail sheath protein / Phage protein / Tail fiber protein
Similarity search - Component
Biological speciesPseudomonas virus Pa193
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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_44166.png

Downloads & links

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Map

FileDownload / File: emd_44166.map.gz / Format: CCP4 / Size: 125 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 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

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: 2.5
Minimum - Maximum-6.0334945 - 14.755628
Average (Standard dev.)-0.000000000001551 (±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_44166_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_44166_additional_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_44166_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44166_half_map_2.map
Projections & Slices
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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: gp32 Sheath
    • Protein or peptide: gp29 Collar
    • Protein or peptide: gp33 Tail tube
    • Protein or peptide: gp30 Gateway

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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: gp32 Sheath

MacromoleculeName: gp32 Sheath / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 53.840039 KDa
SequenceString: MISQSRYIRI ISGVGAGAPV AGRKLILRVM TTNNVIPPGI VIEFDNSNAV MSYFGAQSEE YQRAAAYFKF ISKSVNSPSS ISFARWVNT AIAPMVVGDN LPKTIADFAG FSAGVLTIMV GAAEKNITAI DTSAATSMDN VASIIQTEIR KNTDPQLAQA T VTWNQNTN ...String:
MISQSRYIRI ISGVGAGAPV AGRKLILRVM TTNNVIPPGI VIEFDNSNAV MSYFGAQSEE YQRAAAYFKF ISKSVNSPSS ISFARWVNT AIAPMVVGDN LPKTIADFAG FSAGVLTIMV GAAEKNITAI DTSAATSMDN VASIIQTEIR KNTDPQLAQA T VTWNQNTN QFTLVGATIG TGVLAVAKSA DPQDMSTALG WSTSNVVNVA GQAADLPDAA VAKSTNVSNN FGSFLFAGAP LD NDQIKAV SAWNAAQNNQ FIYTVATSLA NLGTLFDLVK GNAGTGLHVL SATAANDFVE QCPSEIFAAT NYDEPGASQN YMY YQFPGR NITVSDDTVA NTVDKSRGNY IGVTQANGQQ LAFYQRGILC GGPTDAVDMN VYANEIWLKS AIAQALLDLF LNVN AVPAS STGEAMVLAV LQPVLDKATA NGTFTYGKEI SAVQQQYITQ VTGDRRAWRQ VQTLGYWINI TFSSYTNNNT GLIEW KANY TLIYSKGDAI RFVEGSDVMI

UniProtKB: Tail sheath protein

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Macromolecule #2: gp29 Collar

MacromoleculeName: gp29 Collar / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 15.325353 KDa
SequenceString:
MIPGANLLRM AFGVIGTQIV KYRKFEQRVK NDQAQYVSMF EEPFDLAASV QRVRRDQYVQ FNLEFQRNYV MIFANFEMVD LDRDVAGDQ FLWTGRVFQL ESQGSWFYQD GWGVCLAVDI GAAKLTDDGK PTF

UniProtKB: Virion protein

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Macromolecule #3: gp33 Tail tube

MacromoleculeName: gp33 Tail tube / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 15.905042 KDa
SequenceString:
MINISAFGSI CQFTASRTFP NGFTVTEFAD DADPIDSPPF TAADTGVGLN GDMVVWNRAN ILEVVVNVIP NTEGERNLAV LLDANRTGK DKSGARDVVG LVVAMPDGSK ITCTNGTPID GVLINAVASV GRLKTKPYRF RFEKVIKAGT S

UniProtKB: Tail fiber protein

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Macromolecule #4: gp30 Gateway

MacromoleculeName: gp30 Gateway / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 21.204689 KDa
SequenceString:
MFDGELIAKM VVELNAAMTS AQEALQFPDF EVVQKAQPTQ QGTSTRPTIF FQKLFDIPRG WPATDWHLDN TTRKYVEITR QHVETTFQI SSLHWQNPEI THVVTASDIA NYVRAYFQAR STIERVKELD FLILRVSQIS NEAFENDNHQ FEFHPSFDMV V TYNQYIRL YENAAYSADG VLIGV

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: 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: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 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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