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- EMDB-28128: Upper tail structure of Staphylococcus phage Andhra -

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Basic information

Entry
Database: EMDB / ID: EMD-28128
TitleUpper tail structure of Staphylococcus phage Andhra
Map data
Sample
  • Virus: Staphylococcus phage Andhra (virus)
    • Protein or peptide: gp15, receptor-binding protein, tail fiber
    • Protein or peptide: Upper collar protein
    • Protein or peptide: gp16, tail stem protein
    • Protein or peptide: SGNH_hydro domain-containing protein
    • Protein or peptide: gp20, portal-proximal core protein
Keywordsphage tail / portal / receptor-binding protein / VIRUS
Function / homologyPortal 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 speciesStaphylococcus phage Andhra (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsKizziah JL / Hawkins NC / Dokland T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI156636 United States
CitationJournal: 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
DepositionSep 13, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28128.png

Downloads & links

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Map

FileDownload / File: emd_28128.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.328 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.08902089 - 0.13696823
Average (Standard dev.)0.0016012958 (±0.0051179207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 679.936 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28128_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28128_half_map_2.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 : Staphylococcus phage Andhra

EntireName: Staphylococcus phage Andhra (virus)
Components
  • Virus: Staphylococcus phage Andhra (virus)
    • Protein or peptide: gp15, receptor-binding protein, tail fiber
    • Protein or peptide: Upper collar protein
    • Protein or peptide: gp16, tail stem protein
    • Protein or peptide: SGNH_hydro domain-containing protein
    • Protein or peptide: gp20, portal-proximal core protein

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Supramolecule #1: Staphylococcus phage Andhra

SupramoleculeName: 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
Host (natural)Organism: Staphylococcus epidermidis (bacteria)

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Macromolecule #1: gp15, receptor-binding protein, tail fiber

MacromoleculeName: gp15, receptor-binding protein, tail fiber / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 67.393203 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString: 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

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Macromolecule #2: Upper collar protein

MacromoleculeName: Upper collar protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 39.219121 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString: 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

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Macromolecule #3: gp16, tail stem protein

MacromoleculeName: gp16, tail stem protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 33.070457 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString: 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

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Macromolecule #4: SGNH_hydro domain-containing protein

MacromoleculeName: SGNH_hydro domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 46.951672 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString: 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

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Macromolecule #5: gp20, portal-proximal core protein

MacromoleculeName: gp20, portal-proximal core protein / type: protein_or_peptide / ID: 5 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 12.303066 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString:
MAEEEKIIKE EPTNEETEQP EKIESAEDVV TEPEKEVTEE KSEAFVQLEQ RISSLEQRLN NLESQPQPTQ ESSDPNFEDK TVPTEVDDN QETDGIESSE EIKQMLNL

UniProtKB: Adhesin

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154849
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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