Staphylococcus aureus phage 80alpha-derived SaPI1 mature capsid. Sharpened map used for model fitting and refinement. Map sharpened with bsoft by application of inverse Bfactor = 800.
Sample
Virus: Staphylococcus phage 80alpha (virus)
Protein or peptide: Major head protein
Keywords
major capsid protein / HK97-like fold / mature capsid / VIRUS
Function / homology
Phage capsid / Phage capsid family / viral capsid / Major capsid protein
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
R01AI083255
United States
Citation
Journal: Viruses / Year: 2017 Title: Cleavage and Structural Transitions during Maturation of Staphylococcus aureus Bacteriophage 80α and SaPI1 Capsids. Authors: James L Kizziah / Keith A Manning / Altaira D Dearborn / Erin A Wall / Laura Klenow / Rosanne L L Hill / Michael S Spilman / Scott M Stagg / Gail E Christie / Terje Dokland / Abstract: In the tailed bacteriophages, DNA is packaged into spherical procapsids, leading to expansion into angular, thin-walled mature capsids. In many cases, this maturation is accompanied by cleavage of ...In the tailed bacteriophages, DNA is packaged into spherical procapsids, leading to expansion into angular, thin-walled mature capsids. In many cases, this maturation is accompanied by cleavage of the major capsid protein (CP) and other capsid-associated proteins, including the scaffolding protein (SP) that serves as a chaperone for the assembly process. bacteriophage 80α is capable of high frequency mobilization of mobile genetic elements called pathogenicity islands (SaPIs), such as SaPI1. SaPI1 redirects the assembly pathway of 80α to form capsids that are smaller than those normally made by the phage alone. Both CP and SP of 80α are N-terminally processed by a host-encoded protease, Prp. We have analyzed phage mutants that express pre-cleaved or uncleavable versions of CP or SP, and show that the N-terminal sequence in SP is absolutely required for assembly, but does not need to be cleaved in order to produce viable capsids. Mutants with pre-cleaved or uncleavable CP display normal viability. We have used cryo-EM to solve the structures of mature capsids from an 80α mutant expressing uncleavable CP, and from wildtype SaPI1. Comparisons with structures of 80α and SaPI1 procapsids show that capsid maturation involves major conformational changes in CP, consistent with a release of the CP N-arm by SP. The hexamers reorganize during maturation to accommodate the different environments in the 80α and SaPI1 capsids.
History
Deposition
Jan 5, 2018
-
Header (metadata) release
Jan 17, 2018
-
Map release
Jan 17, 2018
-
Update
Mar 13, 2024
-
Current status
Mar 13, 2024
Processing site: RCSB / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
#200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (2)
-
Map
File
Download / File: emd_7333.map.gz / Format: CCP4 / Size: 92.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Staphylococcus aureus phage 80alpha-derived SaPI1 mature capsid. Sharpened map used for model fitting and refinement. Map sharpened with bsoft by application of inverse Bfactor = 800.
Voxel size
X=Y=Z: 2.048 Å
Density
Contour Level
By AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum
-6.673943 - 10.581618000000001
Average (Standard dev.)
-0.000000003075934 (±1.0)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
289
289
289
Spacing
289
289
289
Cell
A=B=C: 591.872 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.048
2.048
2.048
M x/y/z
289
289
289
origin x/y/z
0.000
0.000
0.000
length x/y/z
591.872
591.872
591.872
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
0
0
0
NX/NY/NZ
28
11
56
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
289
289
289
D min/max/mean
-6.674
10.582
-0.000
-
Supplemental data
-
Sample components
-
Entire : Staphylococcus phage 80alpha
Entire
Name: Staphylococcus phage 80alpha (virus)
Components
Virus: Staphylococcus phage 80alpha (virus)
Protein or peptide: Major head protein
-
Supramolecule #1: Staphylococcus phage 80alpha
Supramolecule
Name: Staphylococcus phage 80alpha / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 53369 / Sci species name: Staphylococcus phage 80alpha / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)
Organism: Staphylococcus aureus (bacteria)
Molecular weight
Theoretical: 8.83 MDa
Virus shell
Shell ID: 1 / Name: Capsid / Diameter: 460.0 Å / T number (triangulation number): 4
-
Macromolecule #1: Major head protein
Macromolecule
Name: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi