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- PDB-8ixk: bottom segment of the bacteriophage M13 mini variant -

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Basic information

Entry
Database: PDB / ID: 8ixk
Titlebottom segment of the bacteriophage M13 mini variant
Components
  • Attachment protein G3P
  • Capsid protein G8P
  • Head virion protein G6P
KeywordsVIRAL PROTEIN / Viral coat protein / M13
Function / homology
Function and homology information


viral extrusion / virion attachment to host cell pilus / adhesion receptor-mediated virion attachment to host cell / helical viral capsid / host cell membrane / virion component / viral capsid / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / host cell plasma membrane / membrane
Similarity search - Function
Protein of unknown function DUF5455 / Family of unknown function (DUF5455) / Bacteriophage, G3P, N2-domain superfamily / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P
Similarity search - Domain/homology
Attachment protein G3P / Head virion protein G6P / Capsid protein G8P
Similarity search - Component
Biological speciesInovirus M13
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsXiang, Y. / Jia, Q.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of a bacteriophage M13 mini variant.
Authors: Qi Jia / Ye Xiang /
Abstract: Filamentous bacteriophages package their circular, single stranded DNA genome with the major coat protein pVIII and the minor coat proteins pIII, pVII, pVI, and pIX. Here, we report the cryo-EM ...Filamentous bacteriophages package their circular, single stranded DNA genome with the major coat protein pVIII and the minor coat proteins pIII, pVII, pVI, and pIX. Here, we report the cryo-EM structure of a ~500 Å long bacteriophage M13 mini variant. The distal ends of the mini phage are sealed by two cap-like complexes composed of the minor coat proteins. The top cap complex consists of pVII and pIX, both exhibiting a single helix structure. Arg33 of pVII and Glu29 of pIX, located on the inner surface of the cap, play a key role in recognizing the genome packaging signal. The bottom cap complex is formed by the hook-like structures of pIII and pVI, arranged in helix barrels. Most of the inner ssDNA genome adopts a double helix structure with a similar pitch to that of the A-form double-stranded DNA. These findings provide insights into the assembly of filamentous bacteriophages.
History
DepositionApr 1, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Attachment protein G3P
P: Capsid protein G8P
Q: Capsid protein G8P
S: Capsid protein G8P
Z: Head virion protein G6P
A: Attachment protein G3P
B: Capsid protein G8P
C: Capsid protein G8P
D: Capsid protein G8P
E: Head virion protein G6P
F: Attachment protein G3P
G: Capsid protein G8P
H: Capsid protein G8P
I: Capsid protein G8P
J: Head virion protein G6P
K: Attachment protein G3P
L: Capsid protein G8P
M: Capsid protein G8P
N: Capsid protein G8P
O: Head virion protein G6P
T: Attachment protein G3P
V: Capsid protein G8P
W: Capsid protein G8P
X: Capsid protein G8P
Y: Head virion protein G6P


Theoretical massNumber of molelcules
Total (without water)389,15425
Polymers389,15425
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Attachment protein G3P / Gene 3 protein / G3P / Minor coat protein


Mass: 42573.766 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Inovirus M13 / Gene: III / Production host: Escherichia coli (E. coli) / References: UniProt: P69168
#2: Protein
Capsid protein G8P / / Coat protein B / Gene 8 protein / G8P / M13 procoat / Major coat protein


Mass: 7633.036 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Inovirus M13 / Gene: VIII / Production host: Escherichia coli (E. coli) / References: UniProt: P69541
#3: Protein
Head virion protein G6P / Coat protein D / G6P


Mass: 12357.984 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Inovirus M13 / Gene: VI / Production host: Escherichia coli (E. coli) / References: UniProt: P69532

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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: bottom segment of the bacteriophage M13 mini variant / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Inovirus M13
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Escherichia coli / Strain: TG1
Buffer solutionpH: 8
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1700 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45177 / Symmetry type: POINT

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