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- EMDB-14088: Icosahedral capsid of the phicrAss001 virion -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-14088
TitleIcosahedral capsid of the phicrAss001 virion
Map data
Sample
  • Virus: Bacteroides phage crAss001 (virus)
    • Protein or peptide: Major capsid protein gp32
    • Protein or peptide: Auxiliary capsid protein gp36
    • Protein or peptide: Head fiber trimer protein gp21
    • Protein or peptide: Head fiber dimer protein gp29
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


viral capsid, decoration / virion component / viral capsid / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Bacteriophage B103, Gp8, head fibre / Head fiber protein
Similarity search - Domain/homology
Head fiber trimeric protein / Uncharacterized protein / Auxiliary capsid protein / Major capsid protein
Similarity search - Component
Biological speciesBacteroides phage crAss001 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 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_14088.png

Downloads & links

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Map

FileDownload / File: emd_14088.map.gz / Format: CCP4 / Size: 2.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.36543 Å
Density
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.1023276 - 0.19431096
Average (Standard dev.)0.0004954216 (±0.0075031747)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions916916916
Spacing916916916
CellA=B=C: 1250.7347 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_14088_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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: Major capsid protein gp32
    • Protein or peptide: Auxiliary capsid protein gp36
    • Protein or peptide: Head fiber trimer protein gp21
    • Protein or peptide: Head fiber dimer protein gp29
  • 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-#4 / 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: Major capsid protein gp32

MacromoleculeName: Major capsid protein gp32 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 57.098598 KDa
SequenceString: MAGKLGKFQM LGFQHWKGLT SDNHLGAIFQ QAPQKATNLM VQLLAFYRGK SLDTFLNSFP TREFEDDNEY YWDVIGSSRR NIPLVEARD ENGVVVAANA ANVGVGTSPF YLVFPEDWFA DGEVIVGNLN QVYPFRILGD ARMEGTNAVY KVELMGGNTQ G VPAERLQQ ...String:
MAGKLGKFQM LGFQHWKGLT SDNHLGAIFQ QAPQKATNLM VQLLAFYRGK SLDTFLNSFP TREFEDDNEY YWDVIGSSRR NIPLVEARD ENGVVVAANA ANVGVGTSPF YLVFPEDWFA DGEVIVGNLN QVYPFRILGD ARMEGTNAVY KVELMGGNTQ G VPAERLQQ GERFSIEFAP VEKELSRKVG DVRFTSPVSM RNEWTTIRIQ HKVAGNKLNK KLAMGIPMVR NLESGKQVKD TA NMWMHYV DWEVELQFDE YKNNAMAWGT SNRNLNGEYM NFGKSGNAIK TGAGIFEQTE VANTMYYNTF SLKLLEDALY ELS ASKLAM DDRLFVIKTG ERGAIQFHKE VLKTVSGWTT FVLDNNSTRV VEKVQSRLHS NALSAGFQFV EYKAPNGVRV RLDV DPFYD DPVRNKILHP MGGVAFSYRY DIWYIGTMDQ PNIFKCKIKG DNEYRGYQWG IRNPFTGQKG NPYMSFDEDS AVIHR MATL GVCVLDPTRT MSLIPAILQG

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Macromolecule #2: Auxiliary capsid protein gp36

MacromoleculeName: Auxiliary capsid protein gp36 / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 36.154094 KDa
SequenceString: MVISINQVRQ LYVAKALKAN TAALTTAGDI VPKADTAKTT LYFQSMSPAG IVASDKINLK HVLYAKATPS EALAHKLVRY SVTLDADVS ATPVAGQNYI LRLAFRQYIG LSEEDQYFKY GEVIARSGMT ASDFYKKMAI SLAKNLENKT ESTPLVNIYL I SAAAASTD ...String:
MVISINQVRQ LYVAKALKAN TAALTTAGDI VPKADTAKTT LYFQSMSPAG IVASDKINLK HVLYAKATPS EALAHKLVRY SVTLDADVS ATPVAGQNYI LRLAFRQYIG LSEEDQYFKY GEVIARSGMT ASDFYKKMAI SLAKNLENKT ESTPLVNIYL I SAAAASTD VPVTSATKES DLTATDYNQI IIEETEQPWV LGMMPQAFIP FTPQFLTITV DGEDRLWGVA TVVTPTKTVP DG HLIADLE YFCMGARGDI YRGMGYPNII KTTYLVDPGA VYDVLDIHYF YTGSNESVQK SEKTITLVAV DDGSHTAMNA LIG AINTAS GLTIATL

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Macromolecule #3: Head fiber trimer protein gp21

MacromoleculeName: Head fiber trimer protein gp21 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 13.11096 KDa
SequenceString:
MKRVLNLGNL SRIVEGDPNE ITDDEILVIK DKIIEGKIID IQKRVDGKLV SLITEKYTYT INPTPADAIV VINGSTTKSI RAAKGHTVT WSVSKTGFVT QSGSDVISGD VSKDVTLVAN PAS

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Macromolecule #4: Head fiber dimer protein gp29

MacromoleculeName: Head fiber dimer protein gp29 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 10.294763 KDa
SequenceString:
MKTLRTLKIS PNAPDINSVW LYKGTMKYFN NGEWETIGGE SEPYVLPAAT TSTIGGVKKA TNVGNLATGA ELATVVTKVN AILSALKVA DIMVEDAN

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 51.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 55063
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 152
Output model

PDB-7qof:
Icosahedral capsid of the phicrAss001 virion

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