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- EMDB-28280: In situ cryo-EM structure of Pseudomonas phage E217 tail baseplat... -

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Basic information

Entry
Database: EMDB / ID: EMD-28280
TitleIn situ cryo-EM structure of Pseudomonas phage E217 tail baseplate in C6 map
Map data
Sample
  • Virus: Pseudomonas phage vB_PaeM_E217 (virus)
    • Protein or peptide: Sheath protein gp31
    • Protein or peptide: Structural protein gp33
    • Protein or peptide: Sheath initiator gp34
    • Protein or peptide: Ripcord gp36
    • Protein or peptide: Baseplate_J domain-containing protein gp44
    • Protein or peptide: Structural protein gp45
KeywordsPseudomonas / phage / baseplate / VIRUS
Function / homology
Function and homology information


Protein of unknown function DUF2612 / Protein of unknown function (DUF2612) / Protein of unknown function DUF3383 / Protein of unknown function (DUF3383) / Tail fiber protein gp32 / Baseplate protein J-like / Baseplate J-like protein
Similarity search - Domain/homology
Baseplate protein J-like domain-containing protein / Tail sheath protein / Putative structural protein / Structural protein / Phage protein / Phage protein
Similarity search - Component
Biological speciesPseudomonas phage vB_PaeM_E217 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsLi F / Cingolani G / Hou C
Funding support United States, 1 items
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
DepositionSep 30, 2022-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28280.png

Downloads & links

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Map

FileDownload / File: emd_28280.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.12 Å/pix.
x 400 pix.
= 448. Å		1.12 Å/pix.
x 400 pix.
= 448. Å		1.12 Å/pix.
x 400 pix.
= 448. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.06320333 - 0.0908466
Average (Standard dev.)-0.00011589468 (±0.005056471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 448.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28280_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28280_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pseudomonas phage vB_PaeM_E217

EntireName: Pseudomonas phage vB_PaeM_E217 (virus)
Components
  • Virus: Pseudomonas phage vB_PaeM_E217 (virus)
    • Protein or peptide: Sheath protein gp31
    • Protein or peptide: Structural protein gp33
    • Protein or peptide: Sheath initiator gp34
    • Protein or peptide: Ripcord gp36
    • Protein or peptide: Baseplate_J domain-containing protein gp44
    • Protein or peptide: Structural protein gp45

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Supramolecule #1: Pseudomonas phage vB_PaeM_E217

SupramoleculeName: Pseudomonas phage vB_PaeM_E217 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2034346 / Sci species name: Pseudomonas phage vB_PaeM_E217 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: Sheath protein gp31

MacromoleculeName: Sheath protein gp31 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 53.69475 KDa
SequenceString: MISQSRYIRI ISGVGAAAPV AGRKLILRVM TTNNVIPPGI VIEFDNANAV LSYFGAQSEE YQRAAAYFKF ISKSVNSPSS ISFARWVNT AIAPMVVGDN LPKTIADFAG FSAGVLTIMV GAAEQNITAI DTSAATSMDN VASIIQTEIR KNADPQLAQA T VTWNQNTN ...String:
MISQSRYIRI ISGVGAAAPV AGRKLILRVM TTNNVIPPGI VIEFDNANAV LSYFGAQSEE YQRAAAYFKF ISKSVNSPSS ISFARWVNT AIAPMVVGDN LPKTIADFAG FSAGVLTIMV GAAEQNITAI DTSAATSMDN VASIIQTEIR KNADPQLAQA T VTWNQNTN QFTLVGATIG TGVLAVAKSA DPQDMSTALG WSTSNVVNVA GQSADLPDAA VAKSTNVSNN FGSFLFAGAP LD NDQIKAV SAWNAAQNNQ FIYTVATSLA NLGTLFTLVN GNAGTALNVL SATAANDFVE QCPSEILAAT NYDEPGASQN YMY YQFPGR NITVSDDTVA NTVDKSRGNY IGVTQANGQQ LAFYQRGILC GGPTDAVDMN VYANEIWLKS AIAQALLDLF LNVN AVPAS STGEAMTLAV LQPVLDKATA NGTFTYGKEI SAVQQQYITQ VTGDRRAWRQ VQTLGYWINI TFSSYTNSNT GLTEW KANY TLIYSKGDAI RFVEGSDVMI

UniProtKB: Tail sheath protein

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Macromolecule #2: Structural protein gp33

MacromoleculeName: Structural protein gp33 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 11.575988 KDa
SequenceString:
KIPLTAVPNQ AISFNAGSSY WKIRLYQNMD MMNADISRDG VIVCHGVRCF GGIPLLQYSH QYRPDYGNFV FDRDADWTLF GDGINLFYL DGAEFAEYQA LAT

UniProtKB: Phage protein

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Macromolecule #3: Sheath initiator gp34

MacromoleculeName: Sheath initiator gp34 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 11.769064 KDa
SequenceString:
STSTIRTGTN NDILLDDNGN MVILRDVEAC AQDVRAAMLM RTGENIFDVN SGVGYFEYIF SPQKSYDDAR KSIADAILSS PDVTGIEQL DIDITGEVFG VDAKVITIH

UniProtKB: Phage protein

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Macromolecule #4: Ripcord gp36

MacromoleculeName: Ripcord gp36 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 16.110277 KDa
SequenceString:
MINVSGFGTG IVIVSASSFP MGFSLSKFAD DESPISSKEL EPFGYEMLYD GGLFAFDKAA PLEVSVSVIA GSEDDINLRI LLNSKKGSF RFLPGIIPDM TTLVATLPDG GRTVLSNGTI LKGPAIDTIQ NTGRRKGNTY TFVFGSYLGA QTA

UniProtKB: Structural protein

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Macromolecule #5: Baseplate_J domain-containing protein gp44

MacromoleculeName: Baseplate_J domain-containing protein gp44 / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 43.207457 KDa
SequenceString: MANYNYIVDT GVIVADTADV LSDVEAEFRA ALGANINLAA STPQGSLVAA EAIARSSVMR NEARIANTIN PNVSFGTFLD AICALMGIE RGSDLSTFGY GVQVTGRSQT RISTGSRVQT PAGAIFTVMS DVTIPAGGVA TIDIKSQEYG NIPLPVGNLI I IDGTIGWS ...String:
MANYNYIVDT GVIVADTADV LSDVEAEFRA ALGANINLAA STPQGSLVAA EAIARSSVMR NEARIANTIN PNVSFGTFLD AICALMGIE RGSDLSTFGY GVQVTGRSQT RISTGSRVQT PAGAIFTVMS DVTIPAGGVA TIDIKSQEYG NIPLPVGNLI I IDGTIGWS GAKVIASTRV DPGSRQMSDA ELKNARVNRL AIQGRNSTMA IKAYVSAVPN VTSVNVIENN TGAVQVVNGV SF TLPYAVW VCVAGNPDKQ AVADALWAAH NGGTPWDYGA TNNGVPVDGP NGVPVRDPAS GRKYVVKWTT PIMYDGYVNV TVQ QGSSSV APEAIQNAVV NYAQGKVEGE EGLVVGASLS AFEVAGAIAR EIPGIYIKLC QVACVAAGSP APAPGDFTSE YVMS AFGQA TISVGNVRVT FV

UniProtKB: Baseplate protein J-like domain-containing protein

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Macromolecule #6: Structural protein gp45

MacromoleculeName: Structural protein gp45 / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 54.107535 KDa
SequenceString: LPAYNSDIQQ ALKWLHNQAP GITGLIQRKA QWYDRFSRQF WANWERDVFH LKTANPFGLM VWCIILGTPS KGFGLYPKNS SWAFGRLRQ NFIYSGTQVP PPADASPGGN FYGGGNAEIL NLDEIRKVLQ LRYVALISNG SIAYINRMLR YIFNDDEPWD E ATGLYFYL ...String:
LPAYNSDIQQ ALKWLHNQAP GITGLIQRKA QWYDRFSRQF WANWERDVFH LKTANPFGLM VWCIILGTPS KGFGLYPKNS SWAFGRLRQ NFIYSGTQVP PPADASPGGN FYGGGNAEIL NLDEIRKVLQ LRYVALISNG SIAYINRMLR YIFNDDEPWD E ATGLYFYL MDSTGENGPV ENLAVYRKDW EGMVLLSSSP RTNHVLTSTP ASDADWPGVD PAASGIPVTV ETASATAPDG SA TVCKLTK PAGSTAYVSA PIDGPLGSGS TVTFSFFAKA GSTRFIAIQS AADFPSRADA VFDLDSGNVI SDQMLDSSVV SAR MIRLEN GWWRCVLTTK TVSSSFRAAY VAPAETNFSW IDSNSSAAID VLIWGAQIEL GDTPTGYLKT TGAPVTITDY VLQN AQTGT VKFTQPLPTG VEAYWTGDWK GGTAAEPARF AVGNGTQDTF TLSDPAYIGL PTSGAFKLEY RVGPALNLSP QLINL MNDR AVGIMPTCAG CDVKVI

UniProtKB: Putative structural 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: 8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9300
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 9300
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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