[English] 日本語
Yorodumi
- EMDB-51195: Extended phiCD508 baseplate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51195
TitleExtended phiCD508 baseplate
Map dataC6 helical reconstruction extended phiCD508 baseplate sharpened map (B-factor = -100A)
Sample
  • Complex: Extended phiCD508 baseplate
    • Protein or peptide: gp65 - Triplex 1a protein
    • Protein or peptide: gp66 - Triplex 2 protein
    • Protein or peptide: gp61 - Tail tube initiator
    • Protein or peptide: gp56 - Tail tube protein
    • Protein or peptide: gp55 - Tail sheath protein
    • Protein or peptide: gp64 - Sheath initiator
KeywordsBacteriophage / virus / needle / baseplate
Function / homology
Function and homology information


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 ...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 / 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
Similarity search - Domain/homology
LysM domain/BON superfamily protein / Protein of uncharacterized function (DUF2001) / Phage tail sheath protein / XkdT-related protein / Baseplate J family protein / XkdS-related protein
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 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

-
Structure visualization

Supplemental images

emd_51195.png

Downloads & links

-
Map

FileDownload / File: emd_51195.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC6 helical reconstruction extended phiCD508 baseplate sharpened map (B-factor = -100A)
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: 0.469
Minimum - Maximum-1.0565405 - 2.1894283
Average (Standard dev.)0.005625721 (±0.08861269)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Additional map: C6 helical reconstruction extended phiCD508 baseplate unsharpened map

Fileemd_51195_additional_1.map
AnnotationC6 helical reconstruction extended phiCD508 baseplate unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: C6 helical reconstruction extended phiCD508 baseplate half map A

Fileemd_51195_half_map_1.map
AnnotationC6 helical reconstruction extended phiCD508 baseplate half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: C6 helical reconstruction extended phiCD508 baseplate half map B

Fileemd_51195_half_map_2.map
AnnotationC6 helical reconstruction extended phiCD508 baseplate half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Extended phiCD508 baseplate

EntireName: Extended phiCD508 baseplate
Components
  • Complex: Extended phiCD508 baseplate
    • Protein or peptide: gp65 - Triplex 1a protein
    • Protein or peptide: gp66 - Triplex 2 protein
    • Protein or peptide: gp61 - Tail tube initiator
    • Protein or peptide: gp56 - Tail tube protein
    • Protein or peptide: gp55 - Tail sheath protein
    • Protein or peptide: gp64 - Sheath initiator

-
Supramolecule #1: Extended phiCD508 baseplate

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

-
Macromolecule #1: gp65 - Triplex 1a protein

MacromoleculeName: gp65 - Triplex 1a protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 41.502496 KDa
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

-
Macromolecule #2: gp66 - Triplex 2 protein

MacromoleculeName: gp66 - Triplex 2 protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 23.912678 KDa
SequenceString: MIASKKGKEM LLTLSPIYEQ SIIMQSLYEA IGSEFDNLEL LDEEIELQLF PQSATWGLGF WENRVGLITN LDEDMETRRR KVIAKLQSK YIMTPKRMSM ILQSYTGANI KINENISPYT FGVELTSTQG FPKDLEDLYK RVNVIKPSHL AVSYKLVSLL K SKTYFAQT ...String:
MIASKKGKEM LLTLSPIYEQ SIIMQSLYEA IGSEFDNLEL LDEEIELQLF PQSATWGLGF WENRVGLITN LDEDMETRRR KVIAKLQSK YIMTPKRMSM ILQSYTGANI KINENISPYT FGVELTSTQG FPKDLEDLYK RVNVIKPSHL AVSYKLVSLL K SKTYFAQT AIMSEEITIY PYTSKEVKAS VKAKFALAHN MSSETLTVYP R

UniProtKB: XkdT-related protein

-
Macromolecule #3: gp61 - Tail tube initiator

MacromoleculeName: gp61 - Tail tube initiator / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 25.89983 KDa
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: LysM domain/BON superfamily protein

-
Macromolecule #4: gp56 - Tail tube protein

MacromoleculeName: gp56 - Tail tube protein / type: protein_or_peptide / ID: 4 / 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)

-
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

-
Macromolecule #6: gp64 - Sheath initiator

MacromoleculeName: gp64 - Sheath initiator / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 17.676939 KDa
SequenceString:
MPNLFPQSET FETVELKNND ENELDLKGSF LFDFEKGEFV KNADGTLKKC DKVQAYKQWC QKAILTPRYK KAAYTNIYGS EIKDLIASN LSQSAKELEI TRLIKETILV HPYTKEVGEF SFNWLENSRL VEYEFDVLTI DDENIVIDGN IKR

UniProtKB: XkdS-related protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19276
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more