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- EMDB-4435: Portal and tail of native bacteriophage P68 -

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Basic information

Entry
Database: EMDB / ID: EMD-4435
TitlePortal and tail of native bacteriophage P68
Map dataC12 symmetrized portal and tail of native P68 virion.
Sample
  • Virus: Staphylococcus phage P68 (virus)
    • Complex: Portal protein complex in native virion
      • Protein or peptide: Portal protein
      • Protein or peptide: inner core proteinEarth's inner core
    • Complex: Lower collar protein
      • Protein or peptide: Lower collar protein
    • Complex: Portal protein
    • Complex: Inner core proteinEarth's inner core
    • Complex: Tail fiber protein
      • Protein or peptide: Minor structural protein
Keywordsstructural proteins / bacteriophage portal / bacteriophage tail / native complex / STRUCTURAL PROTEIN
Function / homology
Function and homology information


: / Phage 5-bladed beta propeller receptor binding platform domain / Portal protein Gp10 / Phage Connector (GP10) / Portal protein Gp10 superfamily
Similarity search - Domain/homology
ORF007 / Uncharacterized protein / Upper collar protein / Lower collar protein / Minor structural protein
Similarity search - Component
Biological speciesStaphylococcus phage P68 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHrebik D / Skubnik K
Funding support Czech Republic, 3 items
OrganizationGrant numberCountry
Czech Science Foundation15-21631Y Czech Republic
Czech Science Foundation18-17810S Czech Republic
European Molecular Biology Organization3041 Czech Republic
CitationJournal: Sci Adv / Year: 2019
Title: Structure and genome ejection mechanism of phage P68.
Authors: Dominik Hrebík / Dana Štveráková / Karel Škubník / Tibor Füzik / Roman Pantůček / Pavel Plevka /
Abstract: Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect ...Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect Gram-positive bacteria. Here, we present the structures of native phage P68, genome ejection intermediate, and empty particle. The P68 head contains 72 subunits of inner core protein, 15 of which bind to and alter the structure of adjacent major capsid proteins and thus specify attachment sites for head fibers. Unlike in the previously studied phages, the head fibers of P68 enable its virion to position itself at the cell surface for genome delivery. The unique interaction of one end of P68 DNA with one of the 12 portal protein subunits is disrupted before the genome ejection. The inner core proteins are released together with the DNA and enable the translocation of phage genome across the bacterial membrane into the cytoplasm.
History
DepositionNov 26, 2018-
Header (metadata) releaseNov 6, 2019-
Map releaseNov 6, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.053
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.053
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6iac
  • Surface level: 0.053
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6iac
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4435.png

Downloads & links

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Map

FileDownload / File: emd_4435.map.gz / Format: CCP4 / Size: 262.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC12 symmetrized portal and tail of native P68 virion.
Voxel sizeX=Y=Z: 1.063 Å
Density
Contour LevelBy AUTHOR: 0.053 / Movie #1: 0.053
Minimum - Maximum-0.17900982 - 0.25146338
Average (Standard dev.)0.0006729472 (±0.009550175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-205-2050
Dimensions410410410
Spacing410410410
CellA=B=C: 435.83 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z410410410
origin x/y/z0.0000.0000.000
length x/y/z435.830435.830435.830
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-205-2050
NC/NR/NS410410410
D min/max/mean-0.1790.2510.001

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Supplemental data

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Sample components

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Entire : Staphylococcus phage P68

EntireName: Staphylococcus phage P68 (virus)
Components
  • Virus: Staphylococcus phage P68 (virus)
    • Complex: Portal protein complex in native virion
      • Protein or peptide: Portal protein
      • Protein or peptide: inner core proteinEarth's inner core
    • Complex: Lower collar protein
      • Protein or peptide: Lower collar protein
    • Complex: Portal protein
    • Complex: Inner core proteinEarth's inner core
    • Complex: Tail fiber protein
      • Protein or peptide: Minor structural protein

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Supramolecule #1: Staphylococcus phage P68

SupramoleculeName: Staphylococcus phage P68 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 204090 / Sci species name: Staphylococcus phage P68 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Staphylococcus aureus (bacteria) / Strain: dTarM 4220
Virus shellShell ID: 1 / Name: Capsid / Diameter: 485.0 Å / T number (triangulation number): 4

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Supramolecule #2: Portal protein complex in native virion

SupramoleculeName: Portal protein complex in native virion / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4
Details: portal protein in complex with inner core protein located in the special icosahedral five-fold symmetry vertex
Source (natural)Organism: Staphylococcus phage P68 (virus)

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Supramolecule #3: Lower collar protein

SupramoleculeName: Lower collar protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: lower collar protein is located below the portal protein
Source (natural)Organism: Staphylococcus phage P68 (virus)

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Supramolecule #4: Portal protein

SupramoleculeName: Portal protein / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1
Details: portal protein gp19 located in the special icosahedral five-fold symmetry vertex
Source (natural)Organism: Staphylococcus phage P68 (virus)

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Supramolecule #5: Inner core protein

SupramoleculeName: Inner core protein / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4 / Details: helix of inner core protein located above the wing
Source (natural)Organism: Staphylococcus phage P68 (virus)

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Supramolecule #6: Tail fiber protein

SupramoleculeName: Tail fiber protein / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #3 / Details: Trimer of tail fiber protein
Source (natural)Organism: Staphylococcus phage P68 (virus)

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage P68 (virus)
Molecular weightTheoretical: 37.874699 KDa
SequenceString: MNNDKRGLNV ELSKEISKRV VEHRNRFKRL MFNRYLEFLP LLINYTNRDT VGIDFIQLES ALRQNINVVV GEARNKQIMI LGYVNNTYF NQAPNFSSNF NFQFQKRLTK EDIYFIVPDY LIPDDCLQIH KLYDNCMSGN FVVMQNKPIQ YNSDIEIIEH Y TDELAEVA ...String:
MNNDKRGLNV ELSKEISKRV VEHRNRFKRL MFNRYLEFLP LLINYTNRDT VGIDFIQLES ALRQNINVVV GEARNKQIMI LGYVNNTYF NQAPNFSSNF NFQFQKRLTK EDIYFIVPDY LIPDDCLQIH KLYDNCMSGN FVVMQNKPIQ YNSDIEIIEH Y TDELAEVA LSRFSLIMQA KFSKIFKSEI NDESINQLVS EIYNGAPFVK MSPMFNADDD IIDLTSNSVI PALTEMKREY QN KISELSN YLGINSLAVD KESGVSDEEA KSNRGFTTSN SNIYLKGREP ITFLSKRYGL DIKPYYDDET TSKISMVDTL FKD ESSDIN G

UniProtKB: ORF007

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Macromolecule #2: Lower collar protein

MacromoleculeName: Lower collar protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage P68 (virus)
Molecular weightTheoretical: 29.164445 KDa
SequenceString: MARYTMTLYD FIKSELIKKG FNEFVNDNKL TFYDDEFQFM QKMLKFDKDV LAIVNEKVFK GFSLKDELSD LLFKKSFTIH FLDREINRQ TVEAFGMQVI TVCITHEDYL NVVYSSSEVE KYLQSQGFTE HNEDTTSNTD ETSNQNATSL DNSTGMTANR N AYVSLPQS ...String:
MARYTMTLYD FIKSELIKKG FNEFVNDNKL TFYDDEFQFM QKMLKFDKDV LAIVNEKVFK GFSLKDELSD LLFKKSFTIH FLDREINRQ TVEAFGMQVI TVCITHEDYL NVVYSSSEVE KYLQSQGFTE HNEDTTSNTD ETSNQNATSL DNSTGMTANR N AYVSLPQS EVNIDVDNTT LRFADNNTID NGKTVNKSSN ESNQNAKRNQ NQKGNAKGTQ FTKQYLIDNI DKAYDLRKKI LN EFDKKCF LQIW

UniProtKB: Lower collar protein

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Macromolecule #3: Minor structural protein

MacromoleculeName: Minor structural protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage P68 (virus)
Molecular weightTheoretical: 74.83375 KDa
SequenceString: MAYNENDFKY FDDIRPFLDE IYKTRERYTP FYDDRADYNT NSKSYYDYIS RLSKLIEVLA RRIWDYDNEL KKRFKNWDDL MKAFPEQAK DLFRGWLNDG TIDSIIHDEF KKYSAGLTSA FALFKVTEMK QMNDFKSEVK DLIKDIDRFV NGFELNELEP K FVMGFGGI ...String:
MAYNENDFKY FDDIRPFLDE IYKTRERYTP FYDDRADYNT NSKSYYDYIS RLSKLIEVLA RRIWDYDNEL KKRFKNWDDL MKAFPEQAK DLFRGWLNDG TIDSIIHDEF KKYSAGLTSA FALFKVTEMK QMNDFKSEVK DLIKDIDRFV NGFELNELEP K FVMGFGGI RNAVNQSINI DKETNHMYST QSDSQKPEGF WINKLTPSGD LISSMRIVQG GHGTTIGLER QSNGEMKIWL HH DGVAKLL QVAYKDNYVL DLEEAKGLTD YTPQSLLNKH TFTPLIDEAN DKLILRFGDG TIQVRSRADV KNHIDNVEKE MTI DNSENN DNRWMQGIAV DGDDLYWLSG NSSVNSHVQI GKYSLTTGQK IYDYPFKLSY QDGINFPRDN FKEPEGICIY TNPK TKRKS LLLAMTNGGG GKRFHNLYGF FQLGEYEHFE ALRARGSQNY KLTKDDGRAL SIPDHIDDLN DLTQAGFYYI DGGTA EKLK NMPMNGSKRI IDAGCFINVY PTTQTLGTVQ ELTRFSTGRK MVKMVRGMTL DVFTLKWDYG LWTTIKTDAP YQEYLE ASQ YNNWIAYVTT AGEYYITGNQ MELFRDAPEE IKKVGAWLRV SSGNAVGEVR QTLEANISEY KEFFSNVNAE TKHREYG WV AKHQK

UniProtKB: Minor structural protein

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Macromolecule #4: inner core protein

MacromoleculeName: inner core protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage P68 (virus)
Molecular weightTheoretical: 15.250671 KDa
SequenceString:
MTEFDEIVKP DDKEETSEST EENLESTEET SESTEESTEE STEESTEDKT VETIEEENEN KLEPTTTDED SSKFDPVVLE QRIASLEQQ VTTFLSSQMQ QPQQVQQTQS DVTESNKEDN DYSDEELVDK LDLD

UniProtKB: Uncharacterized protein

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTristris(hydroxymethyl)aminomethane
10.0 mMCaClcalcium chloride
10.0 mMNaClSodium chloridesodium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: NITROGEN
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 2s; blot force -2; 3.6 ul of sample.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-7 / Number grids imaged: 2 / Number real images: 2891 / Average exposure time: 1.0 sec. / Average electron dose: 21.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 37218
Startup modelType of model: INSILICO MODEL
In silico model: the icosahedral initial model was created by a random "de novo" initial model method as described in - Guo F., Jiang W., Methods in molecular biology, 2014.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 6586 / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C12 (12 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 21703
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6iac:
Portal and tail of native bacteriophage P68

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