Journal: Nat Commun / Year: 2019 Title: Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure. Authors: Nicholas P Stone / Gabriel Demo / Emily Agnello / Brian A Kelch / Abstract: The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To ...The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To elucidate how capsids maintain stability in an extreme environment, we use cryoelectron microscopy to determine the capsid structure of thermostable phage P74-26 to 2.8-Å resolution. We find P74-26 capsids exhibit an overall architecture very similar to those of other tailed bacteriophages, allowing us to directly compare structures to derive the structural basis for enhanced stability. Our structure reveals lasso-like interactions that appear to function like catch bonds. This architecture allows the capsid to expand during genome packaging, yet maintain structural stability. The P74-26 capsid has T = 7 geometry despite being twice as large as mesophilic homologs. Capsid capacity is increased with a larger, flatter major capsid protein. Given these results, we predict decreased icosahedral complexity (i.e. T ≤ 7) leads to a more stable capsid assembly.
A: Major head protein B: Major head protein C: Major head protein D: Major head protein E: Major head protein F: Major head protein G: Major head protein H: P74-26 Head Decoration Protein I: P74-26 Head Decoration Protein J: P74-26 Head Decoration Protein K: P74-26 Head Decoration Protein L: P74-26 Head Decoration Protein M: P74-26 Head Decoration Protein N: P74-26 Head Decoration Protein
A: Major head protein B: Major head protein C: Major head protein D: Major head protein E: Major head protein F: Major head protein G: Major head protein H: P74-26 Head Decoration Protein I: P74-26 Head Decoration Protein J: P74-26 Head Decoration Protein K: P74-26 Head Decoration Protein L: P74-26 Head Decoration Protein M: P74-26 Head Decoration Protein N: P74-26 Head Decoration Protein
x 60
complete icosahedral assembly
Evidence: microscopy, Assembly constructed using icosahedral cryoEM reconstruction
A: Major head protein B: Major head protein C: Major head protein D: Major head protein E: Major head protein F: Major head protein G: Major head protein H: P74-26 Head Decoration Protein I: P74-26 Head Decoration Protein J: P74-26 Head Decoration Protein K: P74-26 Head Decoration Protein L: P74-26 Head Decoration Protein M: P74-26 Head Decoration Protein N: P74-26 Head Decoration Protein
x 5
icosahedral pentamer
2.21 MDa, 70 polymers
Theoretical mass
Number of molelcules
Total (without water)
2,207,008
70
Polymers
2,207,008
70
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 head protein B: Major head protein C: Major head protein D: Major head protein E: Major head protein F: Major head protein G: Major head protein H: P74-26 Head Decoration Protein I: P74-26 Head Decoration Protein J: P74-26 Head Decoration Protein K: P74-26 Head Decoration Protein L: P74-26 Head Decoration Protein M: P74-26 Head Decoration Protein N: P74-26 Head Decoration Protein
x 6
icosahedral 23 hexamer
2.65 MDa, 84 polymers
Theoretical mass
Number of molelcules
Total (without water)
2,648,410
84
Polymers
2,648,410
84
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
Majorheadprotein
Mass: 46680.754 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Thermus virus P74-26 / References: UniProt: A7XXR6
#2: Protein
P74-26HeadDecorationProtein
Mass: 16376.630 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Thermus virus P74-26 / References: UniProt: A7XXR5
-
Experimental details
-
Experiment
Experiment
Method: ELECTRON MICROSCOPY
EM experiment
Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction
Electron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 4611
-
Processing
EM software
ID
Name
Version
Category
1
cisTEM
1
particleselection
2
SerialEM
imageacquisition
4
CTFFIND
4
CTFcorrection
7
Coot
0.8
modelfitting
9
FREALIGN
9.11
initialEulerassignment
10
FREALIGN
9.11
finalEulerassignment
11
FREALIGN
9.11
classification
12
FREALIGN
9.11
3Dreconstruction
13
PHENIX
1.14
modelrefinement
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Symmetry
Point symmetry: I (icosahedral)
3D reconstruction
Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23174 / Symmetry type: POINT
Atomic model building
Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation Coefficient
+
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