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- EMDB-28405: Pseudomonas phage E217 baseplate complex -

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Basic information

Entry
Database: EMDB / ID: EMD-28405
TitlePseudomonas phage E217 baseplate complex
Map data
Sample
  • Virus: Pseudomonas phage vB_PaeM_E217 (virus)
    • Protein or peptide: Baseplate component gp33
    • Protein or peptide: Baseplate component gp34
    • Protein or peptide: Baseplate component gp36
    • Protein or peptide: Triplex gp44-b
    • Protein or peptide: Triplex gp45
    • Protein or peptide: Baseplate component gp37
    • Protein or peptide: Baseplate component gp38
    • Protein or peptide: Baseplate hub gp41
    • Protein or peptide: Baseplate spike gp43
KeywordsPseudomonas / phage / baseplate / VIRUS
Function / homology
Function and homology information


Baseplate hub gp41 / Baseplate component gp38 / Protein of unknown function DUF2612 / Protein of unknown function (DUF2612) / Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain / Tail fiber protein gp32 / Baseplate protein J-like / Baseplate J-like protein / Vgr protein, OB-fold domain superfamily
Similarity search - Domain/homology
Baseplate protein J-like domain-containing protein / Phage protein / Tail fiber protein / Phage protein / Phage protein Gp138 N-terminal domain-containing 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: 3.6 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
DepositionOct 3, 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_28405.png

Downloads & links

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Map

FileDownload / File: emd_28405.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 EMDB: 4.36
Minimum - Maximum-6.7664776 - 13.835729000000001
Average (Standard dev.)0.000000000003764 (±1.0)
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_28405_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_28405_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: Baseplate component gp33
    • Protein or peptide: Baseplate component gp34
    • Protein or peptide: Baseplate component gp36
    • Protein or peptide: Triplex gp44-b
    • Protein or peptide: Triplex gp45
    • Protein or peptide: Baseplate component gp37
    • Protein or peptide: Baseplate component gp38
    • Protein or peptide: Baseplate hub gp41
    • Protein or peptide: Baseplate spike gp43

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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: No / Virus empty: No

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Macromolecule #1: Baseplate component gp33

MacromoleculeName: Baseplate component gp33 / type: protein_or_peptide / ID: 1 / 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 #2: Baseplate component gp34

MacromoleculeName: Baseplate component gp34 / type: protein_or_peptide / ID: 2 / 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 #3: Baseplate component gp36

MacromoleculeName: Baseplate component gp36 / type: protein_or_peptide / ID: 3 / 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 #4: Triplex gp44-b

MacromoleculeName: Triplex gp44-b / type: protein_or_peptide / ID: 4 / Number of copies: 12 / 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 #5: Triplex gp45

MacromoleculeName: Triplex gp45 / type: protein_or_peptide / ID: 5 / 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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Macromolecule #6: Baseplate component gp37

MacromoleculeName: Baseplate component gp37 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 19.081869 KDa
SequenceString:
MLGIFTSLLS SRSFSIVDQN TNQLVAADLR ISRVNTRFSS VGQRHMLEDG TTKMDSRTIH PMEIIVEVFC PSIDVVDQIN QLLLDRDTL YKVITRGMVF ERMMCTSEAL NQTPDMISAT PARLTFSQVL VQNPKPIMFR NAGDSSMIDR GLALAEDVVG S AGDLFDYA VNGV

UniProtKB: Phage protein

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Macromolecule #7: Baseplate component gp38

MacromoleculeName: Baseplate component gp38 / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 21.169109 KDa
SequenceString: MNSFLKSILN TPTLTIRDDV TKLPVWKSLQ VKKVEIYSPA SVVSKPLATK DQTEAQVYTE ALDIDVKNGK IIQPVRLRIN AICPDLSTV ESIMNAFNDN TSTFAITSKS ILADKMAIMT LDVDQSPDML NAAEINMEFE QVEPPVLNKF DPAFPQDSPT Y GVQIQSLS ...String:
MNSFLKSILN TPTLTIRDDV TKLPVWKSLQ VKKVEIYSPA SVVSKPLATK DQTEAQVYTE ALDIDVKNGK IIQPVRLRIN AICPDLSTV ESIMNAFNDN TSTFAITSKS ILADKMAIMT LDVDQSPDML NAAEINMEFE QVEPPVLNKF DPAFPQDSPT Y GVQIQSLS DANLLDLGAI GDSISSAAKS LYNRV

UniProtKB: Tail fiber protein

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Macromolecule #8: Baseplate hub gp41

MacromoleculeName: Baseplate hub gp41 / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 32.480277 KDa
SequenceString: MKKRILRVTF NMPYGPEVIR EDLDVRVRIM KAALRIQNRA TMEIFGLTTQ LRESLLSQFT AWKHRQRQVG REDELMIKVS VEAGYSDQG REQVSRVFVG EVAIVDIISP PPDIGIRIQC YTRQIDRTKT IRNMPPANTT FVKFVEWGAN EMGLNFICDT S YNDQVLKN ...String:
MKKRILRVTF NMPYGPEVIR EDLDVRVRIM KAALRIQNRA TMEIFGLTTQ LRESLLSQFT AWKHRQRQVG REDELMIKVS VEAGYSDQG REQVSRVFVG EVAIVDIISP PPDIGIRIQC YTRQIDRTKT IRNMPPANTT FVKFVEWGAN EMGLNFICDT S YNDQVLKN PGRSITVASA ILASIQDMYM PDVAAFVDDD ILIVKDRDKV IRPDEVTNVN SFVGIPSWSE WGVEFQCLFE PS IRVAGGV AVESLMNPSV NGNYVITALE YDLASRDRPF YIKVMGSPAA

UniProtKB: Phage protein

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Macromolecule #9: Baseplate spike gp43

MacromoleculeName: Baseplate spike gp43 / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 23.982912 KDa
SequenceString: NISLTSAKAP DRTRLIAALD ARSRRDALDF EVMIPAQVVQ YDRAENIATI QPLITWVDTE HNAVQRHQLV DIPVISMGAG GFHISFPIQ QGDIGWIYAA DRDTSQFLES LSMSKPNTGR IHKFEHGLFI PDVFRRYTIN SEDSAAMVIQ STSGATRISI R GDNIKITA ...String:
NISLTSAKAP DRTRLIAALD ARSRRDALDF EVMIPAQVVQ YDRAENIATI QPLITWVDTE HNAVQRHQLV DIPVISMGAG GFHISFPIQ QGDIGWIYAA DRDTSQFLES LSMSKPNTGR IHKFEHGLFI PDVFRRYTIN SEDSAAMVIQ STSGATRISI R GDNIKITA PSNVTVDTPQ ANFTGNVTIA NTLVVNGINV NNHGHLENNP PDARTKGGMI A

UniProtKB: Phage protein Gp138 N-terminal domain-containing 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10000
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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