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- EMDB-14089: Portal protein assembly of the phicrAss001 virion with C12 symmet... -
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Open data
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Basic information
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Title | Portal protein assembly of the phicrAss001 virion with C12 symmetry imposed | |||||||||
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![]() | crAssphage / bacteriophage / virus / DNA virus / portal / connector | |||||||||
Function / homology | ![]() virus tail / host cell membrane / virion component / viral capsid / symbiont entry into host cell / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||
![]() | Bayfield OW / Shkoporov AN / Yutin N / Khokhlova EV / Smith JLR / Hawkins DEDP / Koonin EV / Hill C / Antson AA | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 52.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.8 KB 19.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.1 KB | Display | ![]() |
Images | ![]() | 107.9 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 11.2 MB 82.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qogMC ![]() 7qofC ![]() 7qohC ![]() 7qoiC ![]() 7qojC ![]() 7qokC ![]() 7qolC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3941 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_14089_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_14089_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Bacteroides phage crAss001
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Bacteroides phage crAss001
Supramolecule | Name: 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
Macromolecule | Name: Portal protein gp20 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 93.122211 KDa |
Sequence | String: 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 |
-Macromolecule #2: Ring protein 1 gp43
Macromolecule | Name: Ring protein 1 gp43 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 27.479625 KDa |
Sequence | String: 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 |
-Macromolecule #3: Ring protein 2 gp40
Macromolecule | Name: Ring protein 2 gp40 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.216832 KDa |
Sequence | String: 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 |
-Macromolecule #4: Cargo protein 1 gp45
Macromolecule | Name: Cargo protein 1 gp45 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 90.913836 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 51.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 172 |
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Output model | ![]() PDB-7qog: |