+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28128 | |||||||||
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Title | Upper tail structure of Staphylococcus phage Andhra | |||||||||
Map data | ||||||||||
Sample |
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Keywords | phage tail / portal / receptor-binding protein / VIRUS | |||||||||
Function / homology | Portal protein Gp10 superfamily / Autotransporter, pectate lyase C-like domain superfamily / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / SGNH_hydro domain-containing protein / Peptidase S74 domain-containing protein / Adhesin / Upper collar protein Function and homology information | |||||||||
Biological species | Staphylococcus phage Andhra (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.58 Å | |||||||||
Authors | Kizziah JL / Hawkins NC / Dokland T | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structure and host specificity of bacteriophage Andhra. Authors: N'Toia C Hawkins / James L Kizziah / Asma Hatoum-Aslan / Terje Dokland / Abstract: is an opportunistic pathogen of the human skin, often associated with infections of implanted medical devices. Staphylococcal picoviruses are a group of strictly lytic, short-tailed bacteriophages ... is an opportunistic pathogen of the human skin, often associated with infections of implanted medical devices. Staphylococcal picoviruses are a group of strictly lytic, short-tailed bacteriophages with compact genomes that are attractive candidates for therapeutic use. Here, we report the structure of the complete virion of -infecting phage Andhra, determined using high-resolution cryo-electron microscopy, allowing atomic modeling of 11 capsid and tail proteins. The capsid is a = 4 icosahedron containing a unique stabilizing capsid lining protein. The tail includes 12 trimers of a unique receptor binding protein (RBP), a lytic protein that also serves to anchor the RBPs to the tail stem, and a hexameric tail knob that acts as a gatekeeper for DNA ejection. Using structure prediction with AlphaFold, we identified the two proteins that comprise the tail tip heterooctamer. Our findings elucidate critical features for virion assembly, host recognition, and penetration. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28128.map.gz | 463.4 MB | EMDB map data format | |
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Header (meta data) | emd-28128-v30.xml emd-28128.xml | 19.4 KB 19.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28128_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_28128.png | 82 KB | ||
Filedesc metadata | emd-28128.cif.gz | 6.4 KB | ||
Others | emd_28128_half_map_1.map.gz emd_28128_half_map_2.map.gz | 407.1 MB 406.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28128 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28128 | HTTPS FTP |
-Validation report
Summary document | emd_28128_validation.pdf.gz | 954 KB | Display | EMDB validaton report |
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Full document | emd_28128_full_validation.pdf.gz | 953.6 KB | Display | |
Data in XML | emd_28128_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | emd_28128_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28128 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28128 | HTTPS FTP |
-Related structure data
Related structure data | 8egrMC 8egsC 8egtC 8ej5C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28128.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.328 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_28128_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28128_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Staphylococcus phage Andhra
Entire | Name: Staphylococcus phage Andhra (virus) |
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Components |
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-Supramolecule #1: Staphylococcus phage Andhra
Supramolecule | Name: Staphylococcus phage Andhra / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1958907 / Sci species name: Staphylococcus phage Andhra / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Staphylococcus epidermidis (bacteria) |
-Macromolecule #1: gp15, receptor-binding protein, tail fiber
Macromolecule | Name: gp15, receptor-binding protein, tail fiber / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage Andhra (virus) |
Molecular weight | Theoretical: 67.393203 KDa |
Recombinant expression | Organism: Staphylococcus phage Andhra (virus) |
Sequence | String: MYINNGRINY NNEYGYRRGI YREPFYSDNA DYNTNSKSYY DYLARFNGFI FELCDFVNGL ADDIQKMKDT YEALTLSNTD VTYTVGQKG DFDTLNHCFE HIEDLIVQPK SIRVILLKDY MMREQLFLRD KRYNHITITS ENDIVEAYET ELNRQVEIKT N PIFRVKPL ...String: MYINNGRINY NNEYGYRRGI YREPFYSDNA DYNTNSKSYY DYLARFNGFI FELCDFVNGL ADDIQKMKDT YEALTLSNTD VTYTVGQKG DFDTLNHCFE HIEDLIVQPK SIRVILLKDY MMREQLFLRD KRYNHITITS ENDIVEAYET ELNRQVEIKT N PIFRVKPL FYGINSTFPK IDFKLQNKDF SDTINCGFLM DNTTFEMTER GGSTHFNFIG LCGVNGSHIQ TNYCDFSYNG NR EQLEEYN KDQNMYGDGL RIFNSSLTGN YMTVNRCGEI GIHFSHGASG YIDFTEARFN GHHGLMVTTG SQASARNCKI TDT IDDNVV SYASSDIDLR SSDCSNSQTT YGVIATRSSN INFDKGIANG CGASGIMANR GCSIDATGAT ASRNKWHGVI ASNN SKVDF TSGNANENGL DGIQCTHGST VQARLSTTNG NKRNGVLAYA GDVYCQEINC DGNGRRGLEA TRGGYVAAYG AKVSR SKDD NVLAYGSMIS INEALIERAG RNGIEATRGG QIFADRITIT GSGDFGILAY ASKVFAEASN ISGTKNEPVY ATRGGE VTC FGSNISSNKT VYNVYNGSRI FTDKDHGYST NVDPQTLSSK GLIILG UniProtKB: Peptidase S74 domain-containing protein |
-Macromolecule #2: Upper collar protein
Macromolecule | Name: Upper collar protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage Andhra (virus) |
Molecular weight | Theoretical: 39.219121 KDa |
Recombinant expression | Organism: Staphylococcus phage Andhra (virus) |
Sequence | String: MSYLDNDYIG KNKDVGLKVE LTEDIDRRIM EHRNRFRRLI FNRYVEFLPL LINYTNQNSV GIDFLQLEIA LRQGYQVVVG KARNGVIMI LGYIQSMYYK NSNDFINNFN LTFNKRLTQD DITFIIPDYL RPDYALEIEY YDNCQSGDFI VLRNKPVNLN N DYQIIEHY ...String: MSYLDNDYIG KNKDVGLKVE LTEDIDRRIM EHRNRFRRLI FNRYVEFLPL LINYTNQNSV GIDFLQLEIA LRQGYQVVVG KARNGVIMI LGYIQSMYYK NSNDFINNFN LTFNKRLTQD DITFIIPDYL RPDYALEIEY YDNCQSGDFI VLRNKPVNLN N DYQIIEHY CDELAEIILS RFSLIMQSKF SKIFLSDIQD ETINQFINKL YNGAPFIKTD KYIDPEEDII DLGSDFVTTA LV EMKREYQ NKVSELSNFL GVNSLAVDKE SGVSDTEAKS NRSFTTSNSN IYLRGRNPFE MLNRRFNLDI HPYYDDEAIS EMD IMNLKT DNFGGGKVE UniProtKB: Upper collar protein |
-Macromolecule #3: gp16, tail stem protein
Macromolecule | Name: gp16, tail stem protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage Andhra (virus) |
Molecular weight | Theoretical: 33.070457 KDa |
Recombinant expression | Organism: Staphylococcus phage Andhra (virus) |
Sequence | String: LSKHTTTLYE IIESELQRLG LNEFVNNDRI HFNDSKHAFM QKMLYFDDDV KQIVDHMFFK GFMFNDERID RYFKESFTLR FLYREIGRQ TVESFASQVL YITMTHEDYI YRVYGSDMYK YIEQVTDTQS QDLGKAIENA IEQGQTKDRQ QDKGHEEYKD Y EDTITKSF ...String: LSKHTTTLYE IIESELQRLG LNEFVNNDRI HFNDSKHAFM QKMLYFDDDV KQIVDHMFFK GFMFNDERID RYFKESFTLR FLYREIGRQ TVESFASQVL YITMTHEDYI YRVYGSDMYK YIEQVTDTQS QDLGKAIENA IEQGQTKDRQ QDKGHEEYKD Y EDTITKSF DDNRTAESTL PQSKVNIDVD NTVLDYADTN TISRDKNTSE TVSEKTGTKD NTFDSLRNGE SDTKRNTQSQ NE MNRTGLT KQYLIDNLQK LYSMRDTIFK TYDKECFLHI W |
-Macromolecule #4: SGNH_hydro domain-containing protein
Macromolecule | Name: SGNH_hydro domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage Andhra (virus) |
Molecular weight | Theoretical: 46.951672 KDa |
Recombinant expression | Organism: Staphylococcus phage Andhra (virus) |
Sequence | String: LIIKHQMKLH LNELVDWAWR NGVTSEKFHS NNGSYVIFDH SAVVETYIIN KNDLFNVTEE IEITLDKPID YFLEKDMYGN YREHFGIAI NDLLFLNTTV NIWLVNDDNS HILIYKDGKL IDEYMYHQFE YEANQNKHIY PNNKASGTYP HKTEQDVTPP K KQPDTKPL ...String: LIIKHQMKLH LNELVDWAWR NGVTSEKFHS NNGSYVIFDH SAVVETYIIN KNDLFNVTEE IEITLDKPID YFLEKDMYGN YREHFGIAI NDLLFLNTTV NIWLVNDDNS HILIYKDGKL IDEYMYHQFE YEANQNKHIY PNNKASGTYP HKTEQDVTPP K KQPDTKPL PPEEHTPKVR TIKTLNGTVM KDYTPVSSIQ YVKSVGIIGD SVGKGAHASY NFGDYINEKT GAKIQNLSVS SA TMSEVKD NNILNQAKQL KDNELVIIQG TDDDWLFNSN AGVEVGNKIT DTKTYIGAFY KVVETVKENN PKAKIVVITP TKQ AKIDDT GKVIRRDTDK NKKGYTLKTY VDSQVKATKD LGLALYNAYD DSLINPYDEK FRQSSMKDGL HPTKWGHEMM YYRI AETYH KNFD UniProtKB: SGNH_hydro domain-containing protein |
-Macromolecule #5: gp20, portal-proximal core protein
Macromolecule | Name: gp20, portal-proximal core protein / type: protein_or_peptide / ID: 5 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage Andhra (virus) |
Molecular weight | Theoretical: 12.303066 KDa |
Recombinant expression | Organism: Staphylococcus phage Andhra (virus) |
Sequence | String: MAEEEKIIKE EPTNEETEQP EKIESAEDVV TEPEKEVTEE KSEAFVQLEQ RISSLEQRLN NLESQPQPTQ ESSDPNFEDK TVPTEVDDN QETDGIESSE EIKQMLNL UniProtKB: Adhesin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |