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- EMDB-14089: Portal protein assembly of the phicrAss001 virion with C12 symmet... -

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Basic information

Entry
Database: EMDB / ID: EMD-14089
TitlePortal protein assembly of the phicrAss001 virion with C12 symmetry imposed
Map data
Sample
  • Virus: Bacteroides phage crAss001 (virus)
    • Protein or peptide: Portal protein gp20
    • Protein or peptide: Ring protein 1 gp43
    • Protein or peptide: Ring protein 2 gp40
    • Protein or peptide: Cargo protein 1 gp45
KeywordscrAssphage / bacteriophage / virus / DNA virus / portal / connector
Function / homology
Function and homology information


virus tail / host cell membrane / virion component / viral capsid / symbiont entry into host cell / membrane
Similarity search - Function
Portal protein / Ring protein 2 / Ring protein 1 / Cargo protein 1
Similarity search - Component
Biological speciesBacteroides phage crAss001 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 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-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14089.png

Downloads & links

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Map

FileDownload / File: emd_14089.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3941 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.754473 - 1.1770815
Average (Standard dev.)0.0042607314 (±0.038875245)
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_14089_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #2

Fileemd_14089_additional_2.map
Projections & Slices
AxesZYX

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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: Portal protein gp20
    • Protein or peptide: Ring protein 1 gp43
    • Protein or peptide: Ring protein 2 gp40
    • Protein or peptide: Cargo protein 1 gp45

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Supramolecule #1: Bacteroides phage crAss001

SupramoleculeName: Bacteroides phage crAss001 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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: Portal protein gp20

MacromoleculeName: Portal protein gp20 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 93.122211 KDa
SequenceString: MADFLNFPRQ MLPFSKKTKQ WRKDCLLWAN QKTFFNYSLV RKSVIHKKIN YDLLNGRLHM SDLELVLNPD GIKAAYIPDR LQHYPIMNS KLNVLRGEES KRVFDFKVVV TNPNAISEIE DNKKNELLQR LQEMITDTSI SEDEYNIKLE KLNDYYTYEW Q DIREVRAN ...String:
MADFLNFPRQ MLPFSKKTKQ WRKDCLLWAN QKTFFNYSLV RKSVIHKKIN YDLLNGRLHM SDLELVLNPD GIKAAYIPDR LQHYPIMNS KLNVLRGEES KRVFDFKVVV TNPNAISEIE DNKKNELLQR LQEMITDTSI SEDEYNIKLE KLNDYYTYEW Q DIREVRAN ELLNHYIKEY DIPLIFNNGF MDAMTCGEEI YQCDIVGGEP VIERVNPLKI RIFKSGYSNK VEDADMIILE DY WSPGRVI DTYYDVLSPK DIKYIETMPD YIGQGAVDQM DNIDERYGFV NQNMIGDEIT VRDGTYFFDP ANLFTEGIAN SLL PYDLAG NLRVLRLYWK SKRKILKVKS YDPETGEEEW NFYPENYVVN KEAGEEVQSF WVNEAWEGTM IGNEIFVNMR PRLI QYNRL NNPSRCHFGI VGSIYNLNDS RPFSLVDMMK PYNYLYDAIH DRLNKAIASN WGSILELDLS KVPKGWDVGK WMYYA RVNH IAVIDSFKEG TIGASTGKLA GALNNAGKGM IETNIGNYIQ QQINLLEFIK MEMADVAGIS KQREGQISQR ETVGGV ERA TLQSSHITEW LFTIHDDVKK RALECFLETA KVALKGRNKK FQYILSDTST RVMEIDGDEF AEADYGLVVD NSNGTQE LQ QKLDTLAQAA LQTQTLSFST ITKLYTSSSL AEKQRLIEKD EKQIRERQAQ AQKEQLEAQQ QIAAMQQQQK EAELLQKE E ANIRDNQTKI IIAQIQSEGG PDEEDGIMID DYSPEAKANL AEKIREFDEK LKLDKDKLKL DKKKAETDAS IKRQALRKK SSTTNK

UniProtKB: Portal protein

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Macromolecule #2: Ring protein 1 gp43

MacromoleculeName: Ring protein 1 gp43 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 27.479625 KDa
SequenceString: MVNNINWVKL PVILDRLLRH PLLTDLNLET AIQYTLDFIS AMGLPNVYVD KIETIDIKEY RGELPCDLIS INQVRLHKNG IALRAMTDN FNAYPTHDHK EGDWYERGEP SFKTQGRVIF TSIKHEKVDI SYKAIMLDDE GLPLIPDNPI FLKTLELYIK K EWFTILFD ...String:
MVNNINWVKL PVILDRLLRH PLLTDLNLET AIQYTLDFIS AMGLPNVYVD KIETIDIKEY RGELPCDLIS INQVRLHKNG IALRAMTDN FNAYPTHDHK EGDWYERGEP SFKTQGRVIF TSIKHEKVDI SYKAIMLDDE GLPLIPDNPI FLKTLELYIK K EWFTILFD MGKISPAVLN NTQQEYAFKA GQCNNEFVIP SVSEMEAITN MWNQLIPRVT EFRRGFKNLG DKEYIRVH

UniProtKB: Ring protein 1

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Macromolecule #3: Ring protein 2 gp40

MacromoleculeName: Ring protein 2 gp40 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 26.216832 KDa
SequenceString: MTYNELIYMV LDELKLSSDD SYYTPDHVIF LLVKYRSFLL KQRYSDIKKQ IPDSDYQSIC LDLIEVPAIS GEPCEGSSYL RSKNKVPTT MMIGNPRVYP MDFYQGEITY ISRDRMRYVG YNKFLRNIIY CSKAPDGYLY FKSWNPQFLH LEKVSFNAIF E DAKEASEM ...String:
MTYNELIYMV LDELKLSSDD SYYTPDHVIF LLVKYRSFLL KQRYSDIKKQ IPDSDYQSIC LDLIEVPAIS GEPCEGSSYL RSKNKVPTT MMIGNPRVYP MDFYQGEITY ISRDRMRYVG YNKFLRNIIY CSKAPDGYLY FKSWNPQFLH LEKVSFNAIF E DAKEASEM ACPEENGTIC KLEDKEFPIE DALVPPLIEL VVKELRGPEY SPKDEDNNAK DDLPDAR

UniProtKB: Ring protein 2

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Macromolecule #4: Cargo protein 1 gp45

MacromoleculeName: Cargo protein 1 gp45 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 90.913836 KDa
SequenceString: MAKKKIKRRG KMPPNIFDTG GQSWGQQSSG QFSNAFKGEN LGNSIGSIGG AVGGIAQAGI SNAQIADTSG IEAQNKAQKN MVVGASSND DLMSEWGSWN KVKDDYSWKD VRGGSTGQRV TNTIGAAGQG AAAGASVGGP IGAIVGGVVG LGSAIGGWLG G NRKAKRKA ...String:
MAKKKIKRRG KMPPNIFDTG GQSWGQQSSG QFSNAFKGEN LGNSIGSIGG AVGGIAQAGI SNAQIADTSG IEAQNKAQKN MVVGASSND DLMSEWGSWN KVKDDYSWKD VRGGSTGQRV TNTIGAAGQG AAAGASVGGP IGAIVGGVVG LGSAIGGWLG G NRKAKRKA KKLNKEAKEA NERALTSFET RADNIDTQND FNMLANFSAY GGPLEFGSGA IGYEFDNRYL NNQEMSAVAK QR LTSLPNS FQALPEMNTY NAFAEGGGLS REKNYGSKKK PYPSVPSGDF AGPHRSYPIP TKADARDALR LAGLHGNESV RRK VLAKYP SLKAFGGSLF DSVVGNNFNQ SFTQGIQGMF QQEPEQTVQA ANIAKDGGDI KIKEKNKGKF TAYCGGKVTE ACIR KGKNS SNPTTRKRAT FAQNARNWNA FGGWLNTQGG DFTNGVTFIN EGGSHEENPY QGIQIGVDPE GAPNLVEQGE VVYDD YVFS DRMEIPDDIR KEYKLRGKTF AKAAKSAQRE SEERPNDPLS TKGLQAAMER IATAQEEARQ RKEAHREGNE YPSMFA YGG DTNPYGLALE DPMSVEELEA LMVQSGETGE IAPEGNNGNR QTWTRYAPII GSGLASLSDL FSKPDYDSAD LISGVDL GA EAVGYAPIGN YLSYRPLDRD FYINKMNQQA AATRRGLMNT SGGNRLNAQA GILAADYNYG QNMGNLARQA EEYNQQLR E RVEAFNRGTN MFNTETGLKA SMFNAESRNA AKRARLGQAT TVAQLRQGIK DQDAARRSAN ITNFLQGLGD MGWENEQAN WLDTLAKSGV LKMNTKGEYT GGTKKAKGGK VRTKKKKGLT YG

UniProtKB: Cargo protein 1

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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

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 122709
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: 172
Output model

PDB-7qog:
Portal protein assembly of the phicrAss001 virion with C12 symmetry imposed

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