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- EMDB-51200: Extended phiCD508 neck -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51200
TitleExtended phiCD508 neck
Map dataExtended phiCD508 neck sharpened map (B-factor = -86.5A)
Sample
  • Complex: Extended phiCD508 neck
    • Protein or peptide: gp56 - Tail tube protein
    • Protein or peptide: gp51 - Neck valve protein
    • Protein or peptide: gp53 - Tail adaptor protein
    • Protein or peptide: gp50 - Portal adaptor protein
    • Protein or peptide: gp55 - Tail sheath protein
    • Protein or peptide: gp45 - Portal protein
KeywordsBacteriophage / virus / needle / baseplate
Function / homology
Function and homology information


Portal protein / Phage portal protein, SPP1 Gp6-like / Phage tail tube protein / XkdM-like superfamily / Phage tail tube protein / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Putative portal protein / Protein of uncharacterized function (DUF2001) / Phage tail sheath protein / Uncharacterized protein / Phage protein / Phage protein
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWilson JS / Fagan RP / Bullough PA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P02002X/1 United Kingdom
CitationJournal: Life Sci Alliance / Year: 2025
Title: Molecular mechanism of bacteriophage contraction structure of an S-layer-penetrating bacteriophage.
Authors: Jason S Wilson / Louis-Charles Fortier / Robert P Fagan / Per A Bullough /
Abstract: The molecular details of phage tail contraction and bacterial cell envelope penetration remain poorly understood and are completely unknown for phages infecting bacteria enveloped by proteinaceous S- ...The molecular details of phage tail contraction and bacterial cell envelope penetration remain poorly understood and are completely unknown for phages infecting bacteria enveloped by proteinaceous S-layers. Here, we reveal the extended and contracted atomic structures of an intact contractile-tailed phage (φCD508) that binds to and penetrates the protective S-layer of the Gram-positive human pathogen The tail is unusually long (225 nm), and it is also notable that the tail contracts less than those studied in related contractile injection systems such as the model phage T4 (∼20% compared with ∼50%). Surprisingly, we find no evidence of auxiliary enzymatic domains that other phages exploit in cell wall penetration, suggesting that sufficient energy is released upon tail contraction to penetrate the S-layer and the thick cell wall without enzymatic activity. Instead, the unusually long tail length, which becomes more flexible upon contraction, likely contributes toward the required free energy release for envelope penetration.
History
DepositionJul 29, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51200.png

Downloads & links

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Map

FileDownload / File: emd_51200.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExtended phiCD508 neck sharpened map (B-factor = -86.5A)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-0.7509189 - 1.5870092
Average (Standard dev.)-0.0099858 (±0.076608464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Extended phiCD508 neck unsharpened map

Fileemd_51200_additional_1.map
AnnotationExtended phiCD508 neck unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Extended phiCD508 neck half map B

Fileemd_51200_half_map_1.map
AnnotationExtended phiCD508 neck half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Extended phiCD508 neck half map A

Fileemd_51200_half_map_2.map
AnnotationExtended phiCD508 neck half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Extended phiCD508 neck

EntireName: Extended phiCD508 neck
Components
  • Complex: Extended phiCD508 neck
    • Protein or peptide: gp56 - Tail tube protein
    • Protein or peptide: gp51 - Neck valve protein
    • Protein or peptide: gp53 - Tail adaptor protein
    • Protein or peptide: gp50 - Portal adaptor protein
    • Protein or peptide: gp55 - Tail sheath protein
    • Protein or peptide: gp45 - Portal protein

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Supramolecule #1: Extended phiCD508 neck

SupramoleculeName: Extended phiCD508 neck / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117

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Macromolecule #1: gp56 - Tail tube protein

MacromoleculeName: gp56 - Tail tube protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 15.572538 KDa
SequenceString:
MYNDDYIEEA SFLNGSDVVI LIDGVEELYM EEIKADFEQD EQSIKLLGCQ NEISRVGTTK GSFSLNGYKT DSKFAKLGFR SFEIIYNLS NSETLGYESI RLKNCRLKKL PLINSKAGEI VKIEVEGSFR GYDLLNEL

UniProtKB: Protein of uncharacterized function (DUF2001)

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Macromolecule #2: gp51 - Neck valve protein

MacromoleculeName: gp51 - Neck valve protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 14.433568 KDa
SequenceString:
MINIDRRRKD IIRTININPT NITITSIKKT EIDGAFEETE TEIKCVVRIF NEKTAEKQIS SEKQGTFSSI RTYGMLVSND VILEVNSRD SLEFECIYGR MKIVNIYPQI VKGELCGYQC SLERID

UniProtKB: Phage protein

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Macromolecule #3: gp53 - Tail adaptor protein

MacromoleculeName: gp53 - Tail adaptor protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 31.761447 KDa
SequenceString: MRAGIRKALI DNIKELKGCY EPNVPNKDTK KPYMVVVQGQ DNDHGETIGF ERSIEVWIYE GRTTFKKLDK LTKQVVEVLD MNTIVDESE NEAFTCIYKG TSENDIVVEE WDAIARGIRF SVIALEDKED TTNDRWVEAL SRHTKDLLEI ESYKDNWKKN F IAPCALWR ...String:
MRAGIRKALI DNIKELKGCY EPNVPNKDTK KPYMVVVQGQ DNDHGETIGF ERSIEVWIYE GRTTFKKLDK LTKQVVEVLD MNTIVDESE NEAFTCIYKG TSENDIVVEE WDAIARGIRF SVIALEDKED TTNDRWVEAL SRHTKDLLEI ESYKDNWKKN F IAPCALWR TTHIENKRIN YHLIEITKTM KCHVVSKNKD EIVKLLETLE TSLIIDKRVR LREDKNMYLT LVSVVEDRES DM FTTGQLT AVFKMIGKIK REGPTMDKIY GNGNLK

UniProtKB: Uncharacterized protein

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Macromolecule #4: gp50 - Portal adaptor protein

MacromoleculeName: gp50 - Portal adaptor protein / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 12.932699 KDa
SequenceString:
MTPARDLIEK LRLLLNDKDK KSFTDEELNL FLEEADCIYC AASQGWILKS LQYENTVGEM YEYKVGQETY KSSSIKDLVS VAYQNADKF KDMCTNKKEK GSFMLGISTE FEI

UniProtKB: Phage protein

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Macromolecule #5: gp55 - Tail sheath protein

MacromoleculeName: gp55 - Tail sheath protein / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 53.016762 KDa
SequenceString: MATGTWNEKE RKEIPGFYNR FKTQAEKSTN TGLKGRLAMP IRANWGDVGK VVTIKNDLRQ LKNLFGDDMN YSAFKLGKLA LLGNVKELL LYRLVDGNQK KGTLTLKDTT ENSAKDVIKL ETKYPTARNF NVTIKSNLVD SDKKDFIFFE NTKQLFSSSI K GTIDEIVL ...String:
MATGTWNEKE RKEIPGFYNR FKTQAEKSTN TGLKGRLAMP IRANWGDVGK VVTIKNDLRQ LKNLFGDDMN YSAFKLGKLA LLGNVKELL LYRLVDGNQK KGTLTLKDTT ENSAKDVIKL ETKYPTARNF NVTIKSNLVD SDKKDFIFFE NTKQLFSSSI K GTIDEIVL EINSNLDNEY VIATKVADSD TILANVVNQA LEGGNDGCTS ITNESYLKAL EEFERYSFDS FVLDGVADEA LQ ETTKAWV AKNKELGKDI LLFLGGKTED NIKQINDKSK SFNDENIVNV GSSAYYENIK YTPSEVAVYI AALSVSKGIT GSI CNAKTI FEEVEPRLSQ SEVKECLKSG TLVLDFDDGD VIIVDDVNTF KKYVDDKNEA MGYISNIMFI NTINKDTSLK RKEF VGKIF NDATGQTTVI CALKKYFEEL MSQGIISEFN VDIDTELQAT AKADEFYWKW DAVKVDVMKK IYGTGYLG

UniProtKB: Phage tail sheath protein

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Macromolecule #6: gp45 - Portal protein

MacromoleculeName: gp45 - Portal protein / type: protein_or_peptide / ID: 6 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 57.239852 KDa
SequenceString: MGIISYVKKL FKRPAGEIMR MSSGNIGVYK LDDSRVDYEL ARELYQNKNA NYKLGSSFVR PIVNSTTGFM GVPHFQIEDE EAQYILDEF VLDNTSKMLK THTDSLKQGD CYIWITREER ENPLYPDKKV RLIYNFISPE EVKEIILDPT TKEPIAYILE S QNEWTDLG ...String:
MGIISYVKKL FKRPAGEIMR MSSGNIGVYK LDDSRVDYEL ARELYQNKNA NYKLGSSFVR PIVNSTTGFM GVPHFQIEDE EAQYILDEF VLDNTSKMLK THTDSLKQGD CYIWITREER ENPLYPDKKV RLIYNFISPE EVKEIILDPT TKEPIAYILE S QNEWTDLG ENKRKAKVKQ IITAESRFVE VEGDKIEGLE EGETPNVWGF IPIIHFKNEA DETLKYGQSD IEPIEPLLKA YH DVMLHAL KGSKMHSTPK LKLKLTDVAS FLAHNFGVED PVKFAKEGGK INLDGHEILF LNKDEEAEFV EVKSAIGDAK ELL KLLFYC IVDVSETPEF IFGVHTPSAL ASVKEQMPIM VNKIRRKREQ FTNSWQLLAR MVLIMSSNSS GMKYSSYDVT IGWD EVNPR DDKELAETLE KVCCALDKAL EGGFISEEST VNFLAQYIDT MSNYISDDPE REGEREKIIK TKMLKYRLDD SQGLN DESN EIEKEINKIK DNNGNG

UniProtKB: Putative portal 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23724
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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