Journal: Structure / Year: 2019 Title: Capsid Structure of a Freshwater Cyanophage Siphoviridae Mic1. Authors: Hua Jin / Yong-Liang Jiang / Feng Yang / Jun-Tao Zhang / Wei-Fang Li / Ke Zhou / Jue Ju / Yuxing Chen / Cong-Zhao Zhou / Abstract: Cyanobacteria are the most abundant photosynthetic microorganisms, the global distribution of which is mainly regulated by the corresponding cyanophages. A systematic screening of water samples in ...Cyanobacteria are the most abundant photosynthetic microorganisms, the global distribution of which is mainly regulated by the corresponding cyanophages. A systematic screening of water samples in the Lake Chaohu enabled us to isolate a freshwater siphocyanophage that infects Microcystis wesenbergii, thus termed Mic1. Using cryoelectron microscopy, we solved the 3.5-Å structure of Mic1 capsid. The major capsid protein gp40 of an HK97-like fold forms two types of capsomers, hexons and pentons. The capsomers interact with each other via the interweaved N-terminal arms of gp40 in addition to a tail-in-mouth joint along the three-fold symmetric axis, resulting in the assembly of capsid in a mortise-and-tenon pattern. The novel-fold cement protein gp47 sticks at the two-fold symmetric axis and further fixes the capsid. These findings provide structural insights into the assembly of cyanophages, and set up a platform to explore the mechanism of specific interactions and co-evolution with cyanobacteria.
A: major capsid protein B: major capsid protein C: major capsid protein D: major capsid protein E: major capsid protein F: major capsid protein U: major capsid protein V: major capsid protein W: major capsid protein X: major capsid protein Y: major capsid protein Z: major capsid protein a: major capsid protein 0: cement protein 3: cement protein 1: cement protein 4: cement protein 2: cement protein 6: cement protein 5: cement protein 7: cement protein b: cement protein 8: cement protein c: cement protein 9: cement protein d: cement 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 U: major capsid protein V: major capsid protein W: major capsid protein X: major capsid protein Y: major capsid protein Z: major capsid protein a: major capsid protein 0: cement protein 3: cement protein 1: cement protein 4: cement protein 2: cement protein 6: cement protein 5: cement protein 7: cement protein b: cement protein 8: cement protein c: cement protein 9: cement protein d: cement 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 U: major capsid protein V: major capsid protein W: major capsid protein X: major capsid protein Y: major capsid protein Z: major capsid protein a: major capsid protein 0: cement protein 3: cement protein 1: cement protein 4: cement protein 2: cement protein 6: cement protein 5: cement protein 7: cement protein b: cement protein 8: cement protein c: cement protein 9: cement protein d: cement protein
x 5
icosahedral pentamer
3.13 MDa, 130 polymers
Theoretical mass
Number of molelcules
Total (without water)
3,125,102
130
Polymers
3,125,102
130
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 U: major capsid protein V: major capsid protein W: major capsid protein X: major capsid protein Y: major capsid protein Z: major capsid protein a: major capsid protein 0: cement protein 3: cement protein 1: cement protein 4: cement protein 2: cement protein 6: cement protein 5: cement protein 7: cement protein b: cement protein 8: cement protein c: cement protein 9: cement protein d: cement protein
x 6
icosahedral 23 hexamer
3.75 MDa, 156 polymers
Theoretical mass
Number of molelcules
Total (without water)
3,750,122
156
Polymers
3,750,122
156
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
Mass: 37879.035 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Microcystis phage Mic1 (virus) / References: UniProt: A0A4Y5TR23*PLUS
#2: Protein
cementprotein
Mass: 10199.458 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Microcystis phage Mic1 (virus) / References: UniProt: A0A4Y5TPY8*PLUS
-
Experimental details
-
Experiment
Experiment
Method: ELECTRON MICROSCOPY
EM experiment
Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction
Average exposure time: 5.76 sec. / Electron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1935
Image scans
Movie frames/image: 32
-
Processing
EM software
ID
Name
Version
Category
2
SerialEM
imageacquisition
4
CTFFIND
CTFcorrection
7
UCSF Chimera
modelfitting
9
PHENIX
modelrefinement
10
RELION
2
initialEulerassignment
11
RELION
2
finalEulerassignment
12
RELION
2
classification
13
RELION
2
3Dreconstruction
CTF correction
Details: CTFFIND4 / Type: NONE
Particle selection
Num. of particles selected: 18800
Symmetry
Point symmetry: I (icosahedral)
3D reconstruction
Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9702 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model building
Protocol: AB INITIO MODEL
+
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