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- EMDB-24720: SaPIbov5 procapsid structure including size redirecting protein Ccm -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24720 | |||||||||
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Title | SaPIbov5 procapsid structure including size redirecting protein Ccm | |||||||||
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![]() | HK97-like fold / capsid size redirection / major capsid protein / VIRUS | |||||||||
Function / homology | ![]() ATP-dependent peptidase activity / membrane => GO:0016020 / serine-type endopeptidase activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
![]() | Hawkins NC / Kizziah JL | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Shape shifter: redirection of prolate phage capsid assembly by staphylococcal pathogenicity islands. Authors: N'Toia C Hawkins / James L Kizziah / José R Penadés / Terje Dokland / ![]() ![]() Abstract: Staphylococcus aureus pathogenicity islands (SaPIs) are molecular parasites that hijack helper phages for their transfer. SaPIbov5, the prototypical member of a family of cos type SaPIs, redirects ...Staphylococcus aureus pathogenicity islands (SaPIs) are molecular parasites that hijack helper phages for their transfer. SaPIbov5, the prototypical member of a family of cos type SaPIs, redirects the assembly of ϕ12 helper capsids from prolate to isometric. This size and shape shift is dependent on the SaPIbov5-encoded protein Ccm, a homolog of the ϕ12 capsid protein (CP). Using cryo-electron microscopy, we have determined structures of prolate ϕ12 procapsids and isometric SaPIbov5 procapsids. ϕ12 procapsids have icosahedral end caps with T = 4 architecture and a T = 14 cylindrical midsection, whereas SaPIbov5 procapsids have T = 4 icosahedral architecture. We built atomic models for CP and Ccm, and show that Ccm occupies the pentameric capsomers in the isometric SaPIbov5 procapsids, suggesting that preferential incorporation of Ccm pentamers prevents the cylindrical midsection from forming. Our results highlight that pirate elements have evolved diverse mechanisms to suppress phage multiplication, including the acquisition of phage capsid protein homologs. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 470.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.7 KB 14.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.1 KB | Display | ![]() |
Images | ![]() | 181.4 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 5.4 KB | ||
Others | ![]() ![]() | 412 MB 412 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rwzMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_24720_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_24720_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : SaPIbov5 procapsid
Entire | Name: SaPIbov5 procapsid |
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Components |
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-Supramolecule #1: SaPIbov5 procapsid
Supramolecule | Name: SaPIbov5 procapsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Cos capsid morphogenesis protein (Ccm)
Macromolecule | Name: Cos capsid morphogenesis protein (Ccm) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 40.468102 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKIMKEFKEQ FGYQLSNFDD MDIKGYANLY QKDIGKDVSM IEQGLKQLSI TETEVLLPEQ INKKLLGVLN MNEVNQSSNT WVGTLTKQL VSSENNFNIQ ELPTARKEVF KELLVNRELP QTLRDVITIT DDEHVESIPA LSYIKDKLAT NGIELSLNGS S KYFDRREG ...String: MKIMKEFKEQ FGYQLSNFDD MDIKGYANLY QKDIGKDVSM IEQGLKQLSI TETEVLLPEQ INKKLLGVLN MNEVNQSSNT WVGTLTKQL VSSENNFNIQ ELPTARKEVF KELLVNRELP QTLRDVITIT DDEHVESIPA LSYIKDKLAT NGIELSLNGS S KYFDRREG HIYTEVADSV VHGSDRTLDD LLKEIFINEC VSYETTLLLD KNNASGLIDK DNQDLSLYNQ GIKEVSNTSM YD GIKQAMK DIPQTFRRKV SVVMNTEHHD KLIKELAQMG LGTLAGDLTK LFNVSHVVVT DDAQDIFVGD FGHAIYAKYE PIM YNKKKQ ALKGVYQFAL NYVFDIKIVP ELLRIVKVK UniProtKB: Uncharacterized protein |
-Macromolecule #2: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 45.29282 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MRNFKNDNEL LGGNEMPTLY ELKQSLGMIG QQLKNKNDEL SQKATDPNID MEDIKQLETE KAGLQQRFNI VERQVQDIEE KEKAKVKDK GEAYQSLSDN EKMVKAKAEF YRHAILPNEF EKPSMEAQRL LHALPTGNDS GGDKLLPKTL SKEIVSEPFA K NQLREKAR ...String: MRNFKNDNEL LGGNEMPTLY ELKQSLGMIG QQLKNKNDEL SQKATDPNID MEDIKQLETE KAGLQQRFNI VERQVQDIEE KEKAKVKDK GEAYQSLSDN EKMVKAKAEF YRHAILPNEF EKPSMEAQRL LHALPTGNDS GGDKLLPKTL SKEIVSEPFA K NQLREKAR LTNIKGLEIP RVSYTLDDDD FITDVETAKE LKAKGDTVKF TTNKFKVFAA ISDTVIHGSD VDLVNWVENA LQ SGLAAKE RKDALAVSPK SGLEHMSFYN GSVKEVEGAD MYDAIINALA DLHEDYRDNA TIYMRYADYV KIISVLSNGT TNF FDTPAE KVFGKPVVFT DAAVKPIVGD FNYFGINYDG TTYDTDKDVK KGEYLFVLTA WYDQQRTLDS AFRIAKAKEN TGPL PS UniProtKB: ATP-dependent Clp protease proteolytic subunit |
-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: 7.8 |
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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: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |