National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)
R01 GM047795
United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)
S10 OD019995
United States
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Capsid expansion of bacteriophage T5 revealed by high resolution cryoelectron microscopy. Authors: Alexis Huet / Robert L Duda / Pascale Boulanger / James F Conway / Abstract: The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a ...The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a regulated process that involves several intermediates, including a thick-walled round precursor prohead that expands as the viral DNA is packaged to yield a thin-walled and angular mature capsid. We investigated capsid maturation by comparing cryoelectron microscopy (cryo-EM) structures of the prohead, the empty expanded capsid both with and without decoration protein, and the virion capsid at a resolution of 3.8 Å for the latter. We detail the molecular structure of the mcp, its complex pattern of interactions, and their evolution during maturation. The bacteriophage T5 mcp is a variant of the canonical HK97-fold with a high level of plasticity that allows for the precise assembly of a giant macromolecule and the adaptability needed to interact with other proteins and the packaged DNA.
#200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (3)
-
Assembly
Deposited unit
A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein H: Major capsid protein I: Major capsid protein J: Major capsid protein K: Major capsid protein L: Major capsid protein M: Major capsid protein
A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein H: Major capsid protein I: Major capsid protein J: Major capsid protein K: Major capsid protein L: Major capsid protein M: Major capsid protein
A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein H: Major capsid protein I: Major capsid protein J: Major capsid protein K: Major capsid protein L: Major capsid protein M: Major capsid protein
x 5
icosahedral pentamer
2.14 MDa, 65 polymers
Theoretical mass
Number of molelcules
Total (without water)
2,140,538
65
Polymers
2,140,538
65
Non-polymers
0
0
Water
0
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
point symmetry operation
4
4
A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein H: Major capsid protein I: Major capsid protein J: Major capsid protein K: Major capsid protein L: Major capsid protein M: Major capsid protein
x 6
icosahedral 23 hexamer
2.57 MDa, 78 polymers
Theoretical mass
Number of molelcules
Total (without water)
2,568,646
78
Polymers
2,568,646
78
Non-polymers
0
0
Water
0
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
point symmetry operation
5
5
Idetical with deposited unit in distinct coordinate
icosahedral asymmetric unit, std point frame
Type
Name
Symmetry operation
Number
transform to point frame
1
Symmetry
Point symmetry: (Schoenflies symbol: I (icosahedral))
-
Components
#1: Protein
Majorcapsidprotein / Capsid protein pb8 / Major head protein
Mass: 32931.359 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q6QGD8
-
Experimental details
-
Experiment
Experiment
Method: ELECTRON MICROSCOPY
EM experiment
Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction
Electron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3628
-
Processing
EM software
ID
Name
Category
1
X3D
particleselection
2
EPU
imageacquisition
4
CTFFIND
CTFcorrection
7
UCSF Chimera
modelfitting
9
UCSF Chimera
modelrefinement
10
MDFF
modelrefinement
11
PHENIX
modelrefinement
12
Auto3DEM
initialEulerassignment
13
Auto3DEM
finalEulerassignment
15
Auto3DEM
3Dreconstruction
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
Num. of particles selected: 10154
Symmetry
Point symmetry: I (icosahedral)
3D reconstruction
Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8083 / Algorithm: BACK PROJECTION / Symmetry type: POINT
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