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- EMDB-14093: Tail muzzle assembly of the phicrAss001 virion with C6 symmetry i... -

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Basic information

Entry
Database: EMDB / ID: EMD-14093
TitleTail muzzle assembly of the phicrAss001 virion with C6 symmetry imposed
Map data
Sample
  • Virus: Bacteroides phage crAss001 (virus)
    • Protein or peptide: Muzzle protein gp44
    • Protein or peptide: Muzzle bound helix
    • Protein or peptide: Ring protein 4/5 gp34
  • Ligand: MAGNESIUM ION
Function / homologyvirus tail / virion component / Ring protein 4/5 / Muzzle protein
Function and homology information
Biological speciesBacteroides phage crAss001 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsBayfield OW / Shkoporov AN / Yutin N / Khokhlova EV / Smith JLR / Hawkins DEDP / Koonin EV / Hill C / Antson AA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Citation
Journal: Nature / Year: 2023
Title: Structural atlas of a human gut crassvirus.
Authors: Oliver W Bayfield / Andrey N Shkoporov / Natalya Yutin / Ekaterina V Khokhlova / Jake L R Smith / Dorothy E D P Hawkins / Eugene V Koonin / Colin Hill / Alfred A Antson /
Abstract: CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant ...CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals. Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss001, providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the 'crass fold', that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses.
#1: Journal: Res Sq / Year: 2023
Title: Structural atlas of the most abundant human gut virus
Authors: Antson A / Bayfield O / Shkoporov A / Yutin N / Khokhlova E / Smith J / Hawkins D / Koonin E / Hill C
History
DepositionDec 24, 2021-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14093.png

Downloads & links

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Map

FileDownload / File: emd_14093.map.gz / Format: CCP4 / Size: 89.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 286 pix.
= 398.712 Å		1.39 Å/pix.
x 286 pix.
= 398.712 Å		1.39 Å/pix.
x 286 pix.
= 398.712 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3941 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.36477345 - 0.5791251
Average (Standard dev.)-0.00033608422 (±0.02083145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions286286286
Spacing286286286
CellA=B=C: 398.71204 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_14093_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #2

Fileemd_14093_additional_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Bacteroides phage crAss001

EntireName: Bacteroides phage crAss001 (virus)
Components
  • Virus: Bacteroides phage crAss001 (virus)
    • Protein or peptide: Muzzle protein gp44
    • Protein or peptide: Muzzle bound helix
    • Protein or peptide: Ring protein 4/5 gp34
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Bacteroides phage crAss001

SupramoleculeName: Bacteroides phage crAss001 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 2301731 / Sci species name: Bacteroides phage crAss001 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Muzzle protein gp44

MacromoleculeName: Muzzle protein gp44 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 156.459312 KDa
SequenceString: MALKKEQHFF KGMQRDLSVS KFNPEYAFDA QNIRITAREH DTLLSVSNEK GNKEIPLQSP SGDPVVIDGV LLGQNVLNNY VTLFTKGTN DNIYRLENKG TYFETLILFS GNLNFSTDYP IESISVYENN NIQKVYWVDG LNQARVINIT KDDYNNADDF D FVGTIHTS ...String:
MALKKEQHFF KGMQRDLSVS KFNPEYAFDA QNIRITAREH DTLLSVSNEK GNKEIPLQSP SGDPVVIDGV LLGQNVLNNY VTLFTKGTN DNIYRLENKG TYFETLILFS GNLNFSTDYP IESISVYENN NIQKVYWVDG LNQARVINIT KDDYNNADDF D FVGTIHTS SKIEVSKVNG SGAFGQGVIQ YAFTYYNKYG KETNIFRTSP LLYIAYSDRG ASPEETVSCS FQINFTELDS SY DFIRVYS IHRTSIDATP TVRKVADLAT DTKLYVDTGT TGEIVDPTLL LYVGGEEIAP YTMTQKDNTL FLGNYTLKRS LIS TELKNQ IKSDSIVTTI LGGLDDAIES EWNVNTQYNS NYDLNYDSRI KGFQKGEIYR LGIQFQDNKG KWSEVVFIGD YECT ERFKY TQYDTYGITL IPRFKVVISN STTIQAIKNL GYINARGVVV FPTLEDRNIL CQGILCPTVA NYKDRLDNSP FVQSS WFSR PKQATETWKT EYSGTNHLSE FGEVPYFQHN EPIGSASLSE ITRWEIQTSL GLVPYYNPST TNAKDFVDGS PSEFLV DEN IVTMHSPDVE FDDRLQNITN GKFKLRIIGT THLTNTLSDI SVITSTPTYG NYATGFYKGK VANMNISTSY YGGRQLS AG LFWSDNVKFQ DPSPQDKLER LWMVYPWHRN GSLMNMGVPT EGTRAAALQR KIISNLKFAS QNNYLPNQSV WEAEISGD A NHTGITPVNS WTEGLVRIPA QANSNLGSLN YYANIDKVLT FNRSEQISEI YKNGYLIYTT KDWITDGKIA DLFNNAISQ TISVDQVQDW LTRIADTDKY GTEPVSMKYK SNPHLVFAFN YTESGKQLIL PMKNNNNGYL APSANSKPFW NPTAPEGAVY QDSINFTNE NRAFFWLAEL YRDSVVNRFG GDTEEAILNN TWLPSGDSVI IGDSINIEYT EGDTYYQRYD CLRTFAYTNE D QNSIVDIV SFMCESKVNI DGRYDKNRGQ VNNLAVSPTN FNLFNPVYSQ KNNFFTFRTI DYERFSINYF PNSITVTKEK SL GEDIDTW TNITLATTLD LDGDKGEIVS LNTYNNEIFC FQRRGLSNIL FNSRVQIPTS DGMPIEITNG LKVSGKRYIS NTI GCANKW SIAESPSGLY FIDNETNSLY LFNGEIVSLS DKLGFRQWIS THNVHVNWEP VGYNNYRSFY DKNNNDVYFT YKDH CLCYS ELINQFTSFM SYEGVPAMFN VSSEFYAFKD GKMWEQFAGD YNMFFGEYKP FSITFVANAE EPNDKIFNTV EFRAD SWDS DNLISNKTFD TLDVWNEYQH GTTPLTNLLG HPSPLKKKFR IWRANIPRAI ANNRDRIRNT WAYIKLGMNT PNTYRT EFH DAIIHYFA

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Macromolecule #2: Muzzle bound helix

MacromoleculeName: Muzzle bound helix / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 1.209482 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: Ring protein 4/5 gp34

MacromoleculeName: Ring protein 4/5 gp34 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 26.680965 KDa
SequenceString: MNVNEFSNEF DVLYNNIMSN AAPGLNEYEK SVLLTKAQEE IVKNYFEPAG NKYGKGLDDS PKRQIDFSEL IKVGEGVLNT SAPTITFDK RAKVYDLPAD LFLVINEAVD TNAGTKQIVP ISYSDYTRLM SRPYKEPVKY QAWRIITTSI NNISVELIVN S NETITDYK ...String:
MNVNEFSNEF DVLYNNIMSN AAPGLNEYEK SVLLTKAQEE IVKNYFEPAG NKYGKGLDDS PKRQIDFSEL IKVGEGVLNT SAPTITFDK RAKVYDLPAD LFLVINEAVD TNAGTKQIVP ISYSDYTRLM SRPYKEPVKY QAWRIITTSI NNISVELIVN S NETITDYK VRYIRRPAPI ITTNLSSEYG DVTINGVSTV SECELNPIIH SEILQRAVEL AKAAYQGDLQ ASVELGQRSE

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 106962
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 180
Output model

PDB-7qok:
Tail muzzle assembly of the phicrAss001 virion with C6 symmetry imposed

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