[English] 日本語
Yorodumi
- EMDB-43110: C4 pre-infection ejectosome of the mature bacteriophage PhiM1 particle -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43110
TitleC4 pre-infection ejectosome of the mature bacteriophage PhiM1 particle
Map dataPhiM1 ejectosome C4 reconstruction, full map.
Sample
  • Virus: Pectobacterium phage PhiM1 (virus)
    • Protein or peptide: Tetrameric ejection protein (gp48)
    • Protein or peptide: Octameric ejection protein (gp49)
    • Protein or peptide: Ejection protein 3 (gp50)
Keywordsejectosome / internal core / internal proteins / core / mature phage / VIRAL PROTEIN
Function / homologyPutative internal core protein / Internal virion protein B / Putative internal virion protein
Function and homology information
Biological speciesPectobacterium phage PhiM1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsHodgkinson-Bean J / Eruera A
Funding support New Zealand, 1 items
OrganizationGrant numberCountry
Other private New Zealand
CitationJournal: PNAS Nexus / Year: 2024
Title: Ejectosome of bacteriophage ΦM1.
Authors: Alice-Roza Eruera / James Hodgkinson-Bean / Georgia L Rutter / Francesca R Hills / Rosheny Kumaran / Alexander J M Crowe / Nickhil Jadav / Fangfang Chang / Klemens McJarrow-Keller / Fátima ...Authors: Alice-Roza Eruera / James Hodgkinson-Bean / Georgia L Rutter / Francesca R Hills / Rosheny Kumaran / Alexander J M Crowe / Nickhil Jadav / Fangfang Chang / Klemens McJarrow-Keller / Fátima Jorge / Jaekyung Hyun / Hyejin Kim / Bumhan Ryu / Mihnea Bostina /
Abstract: Podophages that infect gram-negative bacteria, such as pathogen ΦM1, encode tail assemblies too short to extend across the complex gram-negative cell wall. To overcome this, podophages encode a ...Podophages that infect gram-negative bacteria, such as pathogen ΦM1, encode tail assemblies too short to extend across the complex gram-negative cell wall. To overcome this, podophages encode a large protein complex (ejectosome) packaged inside the viral capsid and correspondingly ejected during infection to form a transient channel that spans the periplasmic space. Here, we describe the ejectosome of bacteriophage ΦM1 to a resolution of 3.32 Å by single-particle cryo-electron microscopy (cryo-EM). The core consists of tetrameric and octameric ejection proteins which form a ∼1.5-MDa ejectosome that must transition through the ∼30 Å aperture created by the short tail nozzle assembly that acts as the conduit for the passage of DNA during infection. The ejectosome forms several grooves into which coils of genomic DNA are fit before the DNA sharply turns and goes down the tunnel and into the portal. In addition, we reconstructed the icosahedral capsid and hybrid tail apparatus to resolutions between 3.04 and 3.23 Å, and note an uncommon fold adopted by the dimerized decoration proteins which further emphasize the structural diversity of podophages. These reconstructions have allowed the generation of a complete atomic model of the ΦM1, uncovering two distinct decoration proteins and highlighting the exquisite structural diversity of tailed bacteriophages.
History
DepositionDec 11, 2023-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43110.png

Downloads & links

-
Map

FileDownload / File: emd_43110.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhiM1 ejectosome C4 reconstruction, full map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 384 pix.
= 537.6 Å		1.4 Å/pix.
x 384 pix.
= 537.6 Å		1.4 Å/pix.
x 384 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.28
Minimum - Maximum-0.6630469 - 1.1423712
Average (Standard dev.)0.010856176 (±0.057683967)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: PhiM1 ejectosome C4 reconstruction, Half map B.

Fileemd_43110_half_map_1.map
AnnotationPhiM1 ejectosome C4 reconstruction, Half map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: PhiM1 ejectosome C4 reconstruction, Half map A.

Fileemd_43110_half_map_2.map
AnnotationPhiM1 ejectosome C4 reconstruction, Half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Pectobacterium phage PhiM1

EntireName: Pectobacterium phage PhiM1 (virus)
Components
  • Virus: Pectobacterium phage PhiM1 (virus)
    • Protein or peptide: Tetrameric ejection protein (gp48)
    • Protein or peptide: Octameric ejection protein (gp49)
    • Protein or peptide: Ejection protein 3 (gp50)

-
Supramolecule #1: Pectobacterium phage PhiM1

SupramoleculeName: Pectobacterium phage PhiM1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Virus cultured through infection of host Pectobactrium atrocepticum strain SCRI1043.
NCBI-ID: 1211386 / Sci species name: Pectobacterium phage PhiM1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pectobactrium atrocepticum / Strain: SCRI1043
Virus shellShell ID: 1 / Name: Capsid / Diameter: 635.0 Å / T number (triangulation number): 7

-
Macromolecule #1: Tetrameric ejection protein (gp48)

MacromoleculeName: Tetrameric ejection protein (gp48) / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage PhiM1 (virus)
Molecular weightTheoretical: 135.391469 KDa
SequenceString: MIHLRPDSTA YARSAAVSAN PAVGGYVTPD NTVLEGQNPS ALVQAMQKPV ASVTDSFKAT LSESIGAKAL RGVEYASIPT EAGFEPSKA LGDSVSQYTA DELEFLSDAR SSAELAQRRS QVQDTRNNYD AMGQNMLTTV AASMLDVDMV IGGGVGALSK V SRATRLAV ...String:
MIHLRPDSTA YARSAAVSAN PAVGGYVTPD NTVLEGQNPS ALVQAMQKPV ASVTDSFKAT LSESIGAKAL RGVEYASIPT EAGFEPSKA LGDSVSQYTA DELEFLSDAR SSAELAQRRS QVQDTRNNYD AMGQNMLTTV AASMLDVDMV IGGGVGALSK V SRATRLAV GLSANAALLG TASYGGTITP LDVVGTSVGI AMSAIPGIRK VAKAEQVQQG AVRGGVNAAE DAAGTVVPPK DV TVPPVRE VPEVQPIKTV ADEDYPKIDI DTYSNKEHIE VGRTGGAKTG SLKTTVQNAV LAVTALGDDL PEGVRALGRA LGA SLEADA DVPVVFRSRT GANAQARSAV ITEAETGATR AEIFNPAVGG TLSDHVRGMS TYEKTILLHE AAHAKTGRSI RAVE SGAVS DGVVYEAVQR IKEIQWYVKA NVELPPLGKG AKYNVDYGLS DTHEFISQLF NSEHFRDALR SVKMPGSDGT LLSNL MKRV VTLFTGKAPE GNAFDATLQA FDNLLSQPTT PADVFLNAPK ATPDLQSKVL QAPNVIEMNN KVMGALNRNF SLYERL KSF GYKASTLADQ LVVDATGTEA NSAAHHARAA HLASNVSIVQ VDDAFRQALS ADWPLVQRLR HPVLYREAQR DLSQKVY QQ LAENHDRFLK GQSIQPSNDP RVNSMVDAFV NSNWAKDELA RVKGAGINGA DAVRESPYYL PRQHSGNKLN DFMRNNRQ V TKDDIVGMYT EQFSRMFQQN GITPETARKL GAKMFDNMQD QAAHVQGYRQ SIAGMSYDDI ENTLEALGAS DPTITAFLD AVKGSGEQAN KVRNLRGRAE FDMTAQYTTK SGDMISPSMF VNNDVMGLME GYSRRMSGRV GLAKAGFPDL RDAVKAIDEA AAEAQDPAA ALHAFDNTMN QILGYPTGED VPDILRSASI IGGALNLANS GIYQLADMSL MLQQFGITKT LKAFGSTAFG R NAMDVAKS AEFGSRLQDV IEARHVLSGK YRSVLTHLED NRDIGSLGVA HRYVQQMGQG TRFVNGMEFI RRGQAKLVSG LI ADTVDDA IAGNASAVTA MERFGLNQQL LDELRKATAA NPDMRKWPDS VRMDIEAVTH NMADSIVLEN RLGEIPAWMQ FSS VGKVIL PYMTFVAGAW NKILRRTAKL DGATGVAIAL AYQMPLVTLS SATSIAISGK PVTPESVAQR ALVQVPMMSW AGFA VDFWA NGASNNLAAL ALVDRMHAAM SSIASGETNP ESLIKAVPFL SILPGMRLMG ASLADDDE

UniProtKB: Putative internal core protein

-
Macromolecule #2: Octameric ejection protein (gp49)

MacromoleculeName: Octameric ejection protein (gp49) / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage PhiM1 (virus)
Molecular weightTheoretical: 98.011359 KDa
SequenceString: MPVRQPTQGG VQVPGLTGYQ SAGVAQPVYR APQEEAQGVS QFWQNLLPAS VKTAQAAQQT ASAKGYLEGQ QDSQQGREKQ VRNFFTKEA YEQGYNSASV NSALASFQLG LQNTAQQYVN SGKTPEEFNV HVQQQTNQLL QEAGAQGLNL NDKDWQAWLG S VEHSRNTA ...String:
MPVRQPTQGG VQVPGLTGYQ SAGVAQPVYR APQEEAQGVS QFWQNLLPAS VKTAQAAQQT ASAKGYLEGQ QDSQQGREKQ VRNFFTKEA YEQGYNSASV NSALASFQLG LQNTAQQYVN SGKTPEEFNV HVQQQTNQLL QEAGAQGLNL NDKDWQAWLG S VEHSRNTA NASYQDLNLK RAAVLQEQSW GARGNAAIAD FVTAQQSGDT EQALQNVNSF ISSVTHDDSI TAENKIKYTS QF VVNAFAN ANSTGDMQAL TGYVQSLSEF KNMPTDVQTQ IMGSAQQYYQ QRASDESVQL YEYNSRVNSV TDYKTLNEAY PMA QYIGTV MQAVQQKKLS PGTGYGMVDA ESQRRLKMQK AEQGQLAYTN GVTISDIAAG TGESLDKVKG ELTKMYATIG QGYS GGGLQ LMQRGLKSGA QDITGVGIEM MQQDAQSLSG IDWRNLKTDA DGKPLYPAAV VGSLGNLQAA YQSALAAGNQ VQANQ LLSG LPDPVVYGIR QNVDARDLAD VVGKRAQDIA SGKVLALPAN MPADVSITQA DVTAGIFDLG LGKDARNRNM LGIQSW VFT SDADEKAAQA RVSQVNSAMN NEYVYNQQRG SLPALVGDDL KSWLMGKVAS RTVRVKDGTD NGALLVLPEV GDKQKVF GS TDNGIIESAL TESVTNFKKQ YPQATTVQMD YDPLTQELIF QGVNAENQLG TTRASIPAAD FRNTVRGVQN TLTQNGSG T TQGNLNVPGA GFVSFNAGNS FGIQKNVVMG AVNQLVSYEG YTPSKGFSVL GVHPTTGAKL NEDKYVKQAT DTPQVAADK FNMYLNDKVY PLVMPKMEQY KNLPGYIQNN IYNALVETTY HSGNSDVFDK YIQTALYGNV QEIPTFKDTP LFKDAGAGSR RNVDRYQLL GSLVTYRTNN PNLSK

UniProtKB: Internal virion protein B

-
Macromolecule #3: Ejection protein 3 (gp50)

MacromoleculeName: Ejection protein 3 (gp50) / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage PhiM1 (virus)
Molecular weightTheoretical: 21.537678 KDa
SequenceString: MIWMFAAAAA QMIQGGLQYA QDAKNQRRQN KADQKYNEAV RSASARQITE INTQRSVSRA QTAQALDAAR RQGAGESSAR NLQAAATDT MGASVEQNLQ EVGVQLAAAE GNLMQNAELT ELSLDSSVMN TVDQARNSIR ELSNPLGTDW AATGSAVGQI G TSMVANKL ...String:
MIWMFAAAAA QMIQGGLQYA QDAKNQRRQN KADQKYNEAV RSASARQITE INTQRSVSRA QTAQALDAAR RQGAGESSAR NLQAAATDT MGASVEQNLQ EVGVQLAAAE GNLMQNAELT ELSLDSSVMN TVDQARNSIR ELSNPLGTDW AATGSAVGQI G TSMVANKL GGQGWFGGNS GTQQPAPISQ AAPPTRSNNL STRLNV

UniProtKB: Putative internal virion protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration20 mg/mL
BufferpH: 7.4
Details: 10 mM Tris HCl pH 7.4, 10 mM MgSO4 and 0.01% w/v gelatin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: -ve charging.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsSample had a tendency to sit at the edges of holes, or where ice was slightly thicker.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 4429 / Average exposure time: 12.02 sec. / Average electron dose: 53.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.4 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 36765 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.1) / Number images used: 17729
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial models were developed using AlphaFold-2, and were docked into EM maps. Models were then flexibly fit using chimeraX, followed by manual refinement using a combination of ISOLDE (ChimeraX) and coot. Automatic refinements were performed in PHENIX real space refine.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8vb2:
C4 pre-infection ejectosome of the mature bacteriophage PhiM1 particle

+
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