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- PDB-7f38: Cyanophage A-1(L) capsid asymmetric unit -

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Basic information

Entry
Database: PDB / ID: 7f38
TitleCyanophage A-1(L) capsid asymmetric unit
ComponentsPutative major capsid protein
KeywordsVIRUS / Major capsid proteins
Function / homologyPutative major capsid protein
Function and homology information
Biological speciesNostoc phage A1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsCui, N. / Li, Q. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903100 China
CitationJournal: J Virol / Year: 2021
Title: Capsid Structure of Cyanophage A-1(L).
Authors: Ning Cui / Feng Yang / Jun-Tao Zhang / Hui Sun / Yu Chen / Rong-Cheng Yu / Zhi-Peng Chen / Yong-Liang Jiang / Shu-Jing Han / Xudong Xu / Qiong Li / Cong-Zhao Zhou /
Abstract: A-1(L) is a freshwater cyanophage with a contractile tail that specifically infects sp. PCC 7120, one of the model strains for molecular studies of cyanobacteria. Although isolated for half a ...A-1(L) is a freshwater cyanophage with a contractile tail that specifically infects sp. PCC 7120, one of the model strains for molecular studies of cyanobacteria. Although isolated for half a century, its structure remains unknown, which limits our understanding on the interplay between A-1(L) and its host. Here we report the 3.35 Å cryo-EM structure of A-1(L) capsid, representing the first near-atomic resolution structure of a phage capsid with a T number of 9. The major capsid gp4 proteins assemble into 91 capsomers, including 80 hexons: 20 at the center of the facet and 60 at the facet edge, in addition to 11 identical pentons. These capsomers further assemble into the icosahedral capsid, via gradually increasing curvatures. Different from the previously reported capsids of known-structure, A-1(L) adopts a noncovalent chainmail structure of capsid stabilized by two kinds of mortise-and-tenon inter-capsomer interactions: a three-layered interface at the pseudo 3-fold axis combined with the complementarity in shape and electrostatic potential around the 2-fold axis. This unique capsomer construction enables A-1(L) to possess a rigid capsid, which is solely composed of the major capsid proteins with an HK97 fold. Cyanobacteria are the most abundant photosynthetic bacteria, contributing significantly to the biomass production, O generation, and CO consumption on our planet. Their community structure and homeostasis in natural aquatic ecosystems are largely regulated by the corresponding cyanophages. In this study, we solved the structure of cyanophage A-1(L) capsid at near-atomic resolution and revealed a unique capsid construction. This capsid structure provides the molecular details for better understanding the assembly of A-1(L), and a structural platform for future investigation and application of A-1(L) in combination with its host sp. PCC 7120. As the first isolated freshwater cyanophage that infects the genetically tractable model cyanobacterium, A-1(L) should become an ideal template for the genetic engineering and synthetic biology studies.
History
DepositionJun 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • 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
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Putative major capsid protein
B: Putative major capsid protein
C: Putative major capsid protein
D: Putative major capsid protein
E: Putative major capsid protein
F: Putative major capsid protein
G: Putative major capsid protein
H: Putative major capsid protein
I: Putative major capsid protein


Theoretical massNumber of molelcules
Total (without water)355,7229
Polymers355,7229
Non-polymers00
Water0
1
A: Putative major capsid protein
B: Putative major capsid protein
C: Putative major capsid protein
D: Putative major capsid protein
E: Putative major capsid protein
F: Putative major capsid protein
G: Putative major capsid protein
H: Putative major capsid protein
I: Putative major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)21,343,293540
Polymers21,343,293540
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Putative major capsid protein
B: Putative major capsid protein
C: Putative major capsid protein
D: Putative major capsid protein
E: Putative major capsid protein
F: Putative major capsid protein
G: Putative major capsid protein
H: Putative major capsid protein
I: Putative major capsid protein
x 5


  • icosahedral pentamer
  • 1.78 MDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)1,778,60845
Polymers1,778,60845
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Putative major capsid protein
B: Putative major capsid protein
C: Putative major capsid protein
D: Putative major capsid protein
E: Putative major capsid protein
F: Putative major capsid protein
G: Putative major capsid protein
H: Putative major capsid protein
I: Putative major capsid protein
x 6


  • icosahedral 23 hexamer
  • 2.13 MDa, 54 polymers
Theoretical massNumber of molelcules
Total (without water)2,134,32954
Polymers2,134,32954
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
Putative major capsid protein


Mass: 39524.617 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc phage A1 (virus) / Production host: Nostoc phage A1 (virus) / References: UniProt: A0A191SAV5

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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: Nostoc phage A1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Nostoc phage A1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Nostoc sp. PCC 7120 = FACHB-418
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32687 / Symmetry type: POINT

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