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- PDB-6j3q: Capsid structure of a freshwater cyanophage Siphoviridae Mic1 -

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Basic information

Entry
Database: PDB / ID: 6j3q
TitleCapsid structure of a freshwater cyanophage Siphoviridae Mic1
Components
  • cement protein
  • major capsid protein
KeywordsVIRUS / cyanophage / Siphoviridae / capsid
Function / homologyCement / Major capsid protein
Function and homology information
Biological speciesMicrocystis phage Mic1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsJin, H. / Jiang, Y.L. / Yang, F. / Zhang, J.T. / Li, W.F. / Zhou, K. / Ju, J. / Chen, Y. / Zhou, C.Z.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31630001 China
National Natural Science Foundation of China31621002 China
Ministry of Science and Technology (China)2016YFA0400900 China
Chinese Academy of Sciences China
CitationJournal: 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.
History
DepositionJan 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Nov 27, 2019Group: Source and taxonomy / Category: em_entity_assembly_naturalsource / entity_src_nat
Item: _em_entity_assembly_naturalsource.ncbi_tax_id / _em_entity_assembly_naturalsource.organism ..._em_entity_assembly_naturalsource.ncbi_tax_id / _em_entity_assembly_naturalsource.organism / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-9774
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  • Superimposition on EM map
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Structure viewerMolecule:
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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
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


Theoretical massNumber of molelcules
Total (without water)625,02026
Polymers625,02026
Non-polymers00
Water0
1
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 60


Theoretical massNumber of molelcules
Total (without water)37,501,2251560
Polymers37,501,2251560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area130750 Å2
ΔGint-810 kcal/mol
Surface area240390 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
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 massNumber of molelcules
Total (without water)3,125,102130
Polymers3,125,102130
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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 massNumber of molelcules
Total (without water)3,750,122156
Polymers3,750,122156
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
major capsid protein


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
cement protein


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cyanophage / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Microcystis phage Mic1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Microcystis wesenbergii
Virus shellName: gp40 / Diameter: 880 nm / Triangulation number (T number): 13
Buffer solutionpH: 7.5 / Details: 50 mM Tris-HCl pH7.5, 100 mM NaCl, 10 mM MgSO4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
CTF correctionDetails: CTFFIND4 / Type: NONE
Particle selectionNum. of particles selected: 18800
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9702 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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