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- EMDB-51138: C3 reconstruction of extended phiCD508 needle -

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Basic information

Entry
Database: EMDB / ID: EMD-51138
TitleC3 reconstruction of extended phiCD508 needle
Map dataExtended phiCD508 needle sharpened map (Bfactor = -103.9A)
Sample
  • Complex: Extended phiCD508 needle complex
    • Protein or peptide: Baseplate J family protein
    • Protein or peptide: XkdT-related protein
    • Protein or peptide: Peptidoglycan-binding LysM protein
    • Protein or peptide: XkdM-related protein
    • Protein or peptide: Tail sheath
    • Protein or peptide: XkdS-related protein
    • Protein or peptide: Phage protein
    • Protein or peptide: XkdQ-related protein
    • Protein or peptide: Tail tape measure
  • Ligand: FE (II) ION
KeywordsBacteriophage / virus / needle / baseplate
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / viral tail assembly / membrane
Similarity search - Function
Phage tail tape measure protein / Phage-related minor tail protein / : / YQBQ-like / Bacteriophage Mu-like, Gp48 / : / Bacteriophage Mu-like, Gp48 / : / Protein of unknown function DUF2634 / Contractile injection system sheath initiator ...Phage tail tape measure protein / Phage-related minor tail protein / : / YQBQ-like / Bacteriophage Mu-like, Gp48 / : / Bacteriophage Mu-like, Gp48 / : / Protein of unknown function DUF2634 / Contractile injection system sheath initiator / 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 / Baseplate protein J-like / Baseplate J-like protein barrel 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 / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Phage protein / XkdQ-related protein / XkdM-related protein / Peptidoglycan-binding LysM protein / XkdT-related protein / Tail sheath / Baseplate J family protein / Tail tape measure / XkdS-related protein
Similarity search - Component
Biological speciesClostridioides difficile (bacteria) / Clostridioides phage phiCD508 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 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 23, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51138.png

Downloads & links

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Map

FileDownload / File: emd_51138.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExtended phiCD508 needle sharpened map (Bfactor = -103.9A)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 500 pix.
= 530. Å		1.06 Å/pix.
x 500 pix.
= 530. Å		1.06 Å/pix.
x 500 pix.
= 530. 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: 0.0231
Minimum - Maximum-0.051235296 - 0.118146166
Average (Standard dev.)0.00041253964 (±0.0039125504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 530.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: extended phiCD508 needle Half map A

Fileemd_51138_half_map_1.map
Annotationextended phiCD508 needle Half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: extended phiCD508 needle Half map B

Fileemd_51138_half_map_2.map
Annotationextended phiCD508 needle Half map B
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 needle complex

EntireName: Extended phiCD508 needle complex
Components
  • Complex: Extended phiCD508 needle complex
    • Protein or peptide: Baseplate J family protein
    • Protein or peptide: XkdT-related protein
    • Protein or peptide: Peptidoglycan-binding LysM protein
    • Protein or peptide: XkdM-related protein
    • Protein or peptide: Tail sheath
    • Protein or peptide: XkdS-related protein
    • Protein or peptide: Phage protein
    • Protein or peptide: XkdQ-related protein
    • Protein or peptide: Tail tape measure
  • Ligand: FE (II) ION

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Supramolecule #1: Extended phiCD508 needle complex

SupramoleculeName: Extended phiCD508 needle complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117

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Macromolecule #1: Baseplate J family protein

MacromoleculeName: Baseplate J family protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides phage phiCD508 (virus)
Molecular weightTheoretical: 41.502496 KDa
Recombinant expressionOrganism: Clostridioides difficile (bacteria)
SequenceString: MERELPIPVF LTEDEDSVHE RMLSNFQDVS TLEGDFIYDA TRPTAEQIAE LKQLGLQNNL KIAFPQTSYG TYLEWLGECK GVFKNQPTK ATGVITFTGV QGTIITKGTI VTTIATDEKQ SIEFELLETK TIGENETVDI KAESRIVGTI GNVSKGSISV L LGSISGVK ...String:
MERELPIPVF LTEDEDSVHE RMLSNFQDVS TLEGDFIYDA TRPTAEQIAE LKQLGLQNNL KIAFPQTSYG TYLEWLGECK GVFKNQPTK ATGVITFTGV QGTIITKGTI VTTIATDEKQ SIEFELLETK TIGENETVDI KAESRIVGTI GNVSKGSISV L LGSISGVK SITNKEDFRG GTDIEDEEHF RERVLVAEQE DKLSGASSDY IRWAKEVDGV GYAYVVSEWA GAGTVKVLIL DK NRKAATQ ELIDKVQEYI YPLNISEGEN RDGKAPIGAL VTVVTPDTLL INVKASFIFS NGFSEETVLN NLKTKIDKYL DKI DLGGTV SYNAIQAIVG SMMLTDEGIE DFSNLTINDV KENIKLQDQV VGIGEIVNEV VG

UniProtKB: Baseplate J family protein

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Macromolecule #2: XkdT-related protein

MacromoleculeName: XkdT-related protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides phage phiCD508 (virus)
Molecular weightTheoretical: 18.034832 KDa
Recombinant expressionOrganism: Clostridioides difficile (bacteria)
SequenceString:
MIASKKGKEM LLTLSPIYEQ SIIMQSLYEA IGSEFDNLEL LDEEIELQLF PQSATWGLGF WENRVGLITN LDEDMETRRR KVIAKLQSK YIMTPKRMSM ILQSYTGANI KINENISPYT FGVELTSTQG FPKDLEDLYK RVNVIKPSHL AVSYKLVS

UniProtKB: XkdT-related protein

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Macromolecule #3: Peptidoglycan-binding LysM protein

MacromoleculeName: Peptidoglycan-binding LysM protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides phage phiCD508 (virus)
Molecular weightTheoretical: 25.89983 KDa
Recombinant expressionOrganism: Clostridioides difficile (bacteria)
SequenceString: MVIDIYLKNE KEKIDFHFPV NPQDSLSIKK EKRFETVDIV NLGEFDIKKE GEKIREISFK TFLPNLYDAS YCRYSELKNP IEVVAMLEK WVDQAEPLRL IITGFGYNGL VTISSFSNTQ TAGREEDRDI EITFRTYREL KIETLKKDTK SNTKTDLKDN R PNTQTKSK ...String:
MVIDIYLKNE KEKIDFHFPV NPQDSLSIKK EKRFETVDIV NLGEFDIKKE GEKIREISFK TFLPNLYDAS YCRYSELKNP IEVVAMLEK WVDQAEPLRL IITGFGYNGL VTISSFSNTQ TAGREEDRDI EITFRTYREL KIETLKKDTK SNTKTDLKDN R PNTQTKSK IYTVKASDTL YKIAKNLLGK GSRWPEIYNI PENKKVIGKN PNIIKKGQKL VIPSK

UniProtKB: Peptidoglycan-binding LysM protein

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Macromolecule #4: XkdM-related protein

MacromoleculeName: XkdM-related protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides phage phiCD508 (virus)
Molecular weightTheoretical: 14.657557 KDa
Recombinant expressionOrganism: Clostridioides difficile (bacteria)
SequenceString:
EEASFLNGSD VVILIDGVEE LYMEEIKADF EQDEQSIKLL GCQNEISRVG TTKGSFSLNG YKTDSKFAKL GFRSFEIIYN LSNSETLGY ESIRLKNCRL KKLPLINSKA GEIVKIEVEG SFRGYDLLNE L

UniProtKB: XkdM-related protein

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Macromolecule #5: Tail sheath

MacromoleculeName: Tail sheath / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides phage phiCD508 (virus)
Molecular weightTheoretical: 51.405023 KDa
Recombinant expressionOrganism: Clostridioides difficile (bacteria)
SequenceString: EIPGFYNRFK AQAEKAAATG LKGRLAMPIR ANWGDVGKVV TIKNDLRQLK NLFGDDMNYS AFKLGKLALL GNVKELLLYR LVDGNQKKG TLTLKDTTEN SAKDVIKLET KYPTARNFNV TIKSNLVDSD KKDFIFFENT KQLFSSSIKG TIDEIVLEIN S NLDNEYVI ...String:
EIPGFYNRFK AQAEKAAATG LKGRLAMPIR ANWGDVGKVV TIKNDLRQLK NLFGDDMNYS AFKLGKLALL GNVKELLLYR LVDGNQKKG TLTLKDTTEN SAKDVIKLET KYPTARNFNV TIKSNLVDSD KKDFIFFENT KQLFSSSIKG TIDEIVLEIN S NLDNEYVI ATKVADSDTI LANVVNQALE GGNDGCTSIT NESYLKALEE FERYSFDSFV LDGVADEALQ ETTKAWVAKN KE LGKDILL FLGGKTEDNI KQINDKSKSF NDENIVNVGS SAYYENIKYT PSEVAVYIAA LSVSKGITGS ICNAKTIFEE VEP RLSQSE VKECLKSGTL VLDFDDGDVI IVDDVNTFKK YVDDKNEAMG YISNIMFINT INKDTSLKRK EFVGKIFNDA TGQT TVICA LKKYFEELMS QGIISEFNVD IDTELQATAK ADEFYWKWDA VKVDVMKKIY GTGYL

UniProtKB: Tail sheath

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Macromolecule #6: XkdS-related protein

MacromoleculeName: XkdS-related protein / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides phage phiCD508 (virus)
Molecular weightTheoretical: 14.454414 KDa
Recombinant expressionOrganism: Clostridioides difficile (bacteria)
SequenceString:
LDLKGSFLFD FEKGEFVKNA DGTLKKCDKV QAYKQWCQKA ILTPRYKKAA YTNIYGSEIK DLIASNLSQS AKELEITRLI KETILVHPY TKEVGEFSFN WLENSRLVEY EFDVLTIDDE NIVIDG

UniProtKB: XkdS-related protein

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Macromolecule #7: Phage protein

MacromoleculeName: Phage protein / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides phage phiCD508 (virus)
Molecular weightTheoretical: 12.476309 KDa
Recombinant expressionOrganism: Clostridioides difficile (bacteria)
SequenceString:
FNGIARILKE NMNKSVANGT FGMGCELAEI TANGLKVNGY KDEIQDYLVL ENLTLKEDYF TFSDEALSGE YRHKHKIETP KELKPLRIG DNVLVAVMGA EFVVIGRVVN AKP

UniProtKB: Phage protein

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Macromolecule #8: XkdQ-related protein

MacromoleculeName: XkdQ-related protein / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides phage phiCD508 (virus)
Molecular weightTheoretical: 36.291719 KDa
Recombinant expressionOrganism: Clostridioides difficile (bacteria)
SequenceString: KIILNGKYDI ANFNEGITLS EAIDGVAYKM DVSLVEPKQL KDINIKKGDK IILIDIAYES KKEETIFDGV VWETRRSEKS KKLTLSCRE RTVYMEESEE QYQFKENTAT QRIEYYCKQW NIPYYNLANT GKKLAKVIHK TNILDMIKKD LKETATKGGD L FRVRMDNK ...String:
KIILNGKYDI ANFNEGITLS EAIDGVAYKM DVSLVEPKQL KDINIKKGDK IILIDIAYES KKEETIFDGV VWETRRSEKS KKLTLSCRE RTVYMEESEE QYQFKENTAT QRIEYYCKQW NIPYYNLANT GKKLAKVIHK TNILDMIKKD LKETATKGGD L FRVRMDNK LKLFKLGTNA NVYKLDSILE DANFTSSFND AVTSVKVLGK SKDENTKAPI IGTYKKDADK FGTLQKIKQD EK IKNAKEA KKAAEAMFNS GEETISVDCA VDINRIRAGD KVSLKSKEYY VIDVTHTLDS RPKMKLNIGS LEYIRRKFY

UniProtKB: XkdQ-related protein

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Macromolecule #9: Tail tape measure

MacromoleculeName: Tail tape measure / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides phage phiCD508 (virus)
Molecular weightTheoretical: 150.075156 KDa
Recombinant expressionOrganism: Clostridioides difficile (bacteria)
SequenceString: MREIAKKEMY HIDVVISAKG DGETKSKLSA MEKYMKQTEK RMQTLNRIKV NPAIKATDKA SSVVNRVNNN MNKAKKTVTA RIKATDNAS PVANRASNNV NKAKKTVTAR LKATDNASST VNKVNNKIKE VAKPVPPVII RGQDESSSII DKVKAKIQNL K ADTIIKIK ...String:
MREIAKKEMY HIDVVISAKG DGETKSKLSA MEKYMKQTEK RMQTLNRIKV NPAIKATDKA SSVVNRVNNN MNKAKKTVTA RIKATDNAS PVANRASNNV NKAKKTVTAR LKATDNASST VNKVNNKIKE VAKPVPPVII RGQDESSSII DKVKAKIQNL K ADTIIKIK SQADEAINTI SRTKNKLQEF VSKRYEAAVK IRDEASSALR GLTGKIDSFV SGAISKFARL ATTAGALIGG IG VGSAVKG FATFEQSMKN TQAVSGATGK EMEALTAKAR QLGRETSFTA KDAGDAMYYM GMAGWKSEQM IKAIPDVLNL AAA GGTDLA LTSDIVTDGL TALGMTANDT TEFVDVMAAT ITNSNTSVEL MGETFKYVGS MGGALGVSMK DLSLATGLMA SASV KGSMA GTSLRGGLVR LIKPPEEAAS AIKKYGIELK KNKNGSLDLA GTIGSLREKL GGLKDVEKGV AISSIFGRTA MAGWA AVVN ASESDFNKLT TAIAESEGEA KRIADMKLDT LSGQFEILKS AIDDVRISVG QRLGPMTRGF VEDLIKKMPQ IGDAIV GVV EKFVNNFDKI KAGFQVLLPA IGSVIASVMV LKATFAFGGA IKSLSLLAST FGTAKLVAFG LTVGIGAIVI AFAGMTV AI SNNKTAMMDL QTRFGSFGEY VTTIMETVGG VIKLTLGNLL IMLGGIGKGI GILLSDKSWD EKASSLKNLF GKTTAEIK T NTKEALSDIN GETSNATALL KKSTSKELQG VTKAFSTAFD QSKNVTEKKS SDIARALTNG LKGLDDQSLT MMRGLNDNM AIILSGVTAD MKPSDKVNKI TKNLDDAFKA GKLSAQEYRS SIQETLNFIS KYSADSSNNL KQGMSDAFNA FKEGTNIGGL KDGVTGMLN SLKATGPQAL ETLKGLGGKA SEIFKGVDFN SSIDAQKTKV LQNLNSLGLE GTQAIDTLRT IFSQASSALD T TNLKQGLS NTFNSFKEGF NSGGIKNAIN SMLGTINQAG PQMQQALGKM DGKMGQVFAN VDFSTPIETQ ASKVLENLNN LG IEGPKAL ETVRSIFAQA SSQIQGSASQ TAQQANQEVA NALTQGNPAV QQAGQQLGTD LTNGVVNGVQ AGVPVVQQKS NEL ATATQN GVTNAVNSAT PQIDNSNLTS GIDTAFNQAT ATVQQGASSM YNGAKQSFTQ LAQIGREAGS SLYNGATTSF NMLA TNVRV ACSSMYNGAR TSFTSLSSSA ISAISAMCSS VVSQVSAMSS QIISYWNSVR ATVSAPITAS FNVKTTQTTV KRTVN ESSG GILGNILDRF ADGGVATRTS ICGENGAEMV IPLTNTRRSR AIELYEQTGK MLGLGSTPSQ KVGNSNIVNN VRQFPL ANV LDTDNKEYKE ATPNSVNSSN NTINLGGISI NVQNSDNKEE MIQELLSQVE SGIREALQDI G

UniProtKB: Tail tape measure

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Macromolecule #10: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
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 / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17759
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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