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- PDB-7xdi: Tail structure of bacteriophage SSV19 -

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Basic information

Entry
Database: PDB / ID: 7xdi
TitleTail structure of bacteriophage SSV19
Components
  • B210
  • C131
  • VP1
  • VP4
KeywordsVIRAL PROTEIN / Complex
Function / homology
Function and homology information


membrane => GO:0016020 / carbohydrate metabolic process / structural molecule activity
Similarity search - Function
Structural protein VP1/VP3 / Structural protein VP1/VP3 / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
VP4 / Uncharacterized protein / Uncharacterized protein / VP1
Similarity search - Component
Biological speciesSulfolobus spindle-shaped virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLiu, H.R. / Chen, W.Y.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)31970170 China
National Natural Science Foundation of China (NSFC)91951000 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)31971122 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural insights into a spindle-shaped archaeal virus with a sevenfold symmetrical tail.
Authors: Zhen Han / Wanjuan Yuan / Hao Xiao / Li Wang / Junxia Zhang / Yuning Peng / Lingpeng Cheng / Hongrong Liu / Li Huang /
Abstract: Archaeal viruses with a spindle-shaped virion are abundant and widespread in extremely diverse environments. However, efforts to obtain the high-resolution structure of a spindle-shaped virus have ...Archaeal viruses with a spindle-shaped virion are abundant and widespread in extremely diverse environments. However, efforts to obtain the high-resolution structure of a spindle-shaped virus have been unsuccessful. Here, we present the structure of SSV19, a spindle-shaped virus infecting the hyperthermophilic archaeon sp. E11-6. Our near-atomic structure reveals an unusual sevenfold symmetrical virus tail consisting of the tailspike, nozzle, and adaptor proteins. The spindle-shaped capsid shell is formed by seven left-handed helical strands, constructed of the hydrophobic major capsid protein, emanating from the highly glycosylated tail assembly. Sliding between adjacent strands is responsible for the variation of a virion in size. Ultrathin sections of the SSV19-infected cells show that SSV19 virions adsorb to the host cell membrane through the tail after penetrating the S-layer. The tailspike harbors a putative endo-mannanase domain, which shares structural similarity to a endo-mannanase. Molecules of glycerol dibiphytanyl glycerol tetraether lipid were observed in hydrophobic clefts between the tail and the capsid shell. The nozzle protein resembles the stem and clip domains of the portals of herpesviruses and bacteriophages, implying an evolutionary relationship among the archaeal, bacterial, and eukaryotic viruses.
History
DepositionMar 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP1
C: VP1
D: C131
E: B210
F: VP4


Theoretical massNumber of molelcules
Total (without water)202,8686
Polymers202,8686
Non-polymers00
Water0
1
A: VP1
B: VP1
C: VP1
D: C131
E: B210
F: VP4
x 7


Theoretical massNumber of molelcules
Total (without water)1,420,07742
Polymers1,420,07742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation6
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C7 (7 fold cyclic))

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Components

#1: Protein VP1


Mass: 9282.206 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sulfolobus spindle-shaped virus / References: UniProt: A0A5Q0V137
#2: Protein C131


Mass: 14753.507 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sulfolobus spindle-shaped virus / References: UniProt: A0A5Q0V0G9
#3: Protein B210


Mass: 23195.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sulfolobus spindle-shaped virus / References: UniProt: A0A5Q0V0F6
#4: Protein VP4


Mass: 137071.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sulfolobus spindle-shaped virus / References: UniProt: A0A5Q0V0A2

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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: Sulfolobus spindle-shaped virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Sulfolobus spindle-shaped virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49361 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037879
ELECTRON MICROSCOPYf_angle_d0.69610813
ELECTRON MICROSCOPYf_dihedral_angle_d4.5991035
ELECTRON MICROSCOPYf_chiral_restr0.0431290
ELECTRON MICROSCOPYf_plane_restr0.0061321

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