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- PDB-8ixj: Middle segment of the bacteriophage M13 mini variant -

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Basic information

Entry
Database: PDB / ID: 8ixj
TitleMiddle segment of the bacteriophage M13 mini variant
ComponentsCapsid protein G8P
KeywordsVIRAL PROTEIN / Viral coat protein / M13
Function / homologyPhage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / helical viral capsid / host cell plasma membrane / membrane / Capsid protein G8P
Function and homology information
Biological speciesInovirus M13
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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 1.0Aug 16, 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
B: Capsid protein G8P
C: Capsid protein G8P
L: Capsid protein G8P
F: Capsid protein G8P
G: Capsid protein G8P
H: Capsid protein G8P
I: Capsid protein G8P
J: Capsid protein G8P
A: Capsid protein G8P
D: Capsid protein G8P
E: Capsid protein G8P
K: Capsid protein G8P
M: Capsid protein G8P
N: Capsid protein G8P
O: Capsid protein G8P
P: Capsid protein G8P
Q: Capsid protein G8P
R: Capsid protein G8P
S: Capsid protein G8P
T: Capsid protein G8P
V: Capsid protein G8P
W: Capsid protein G8P
X: Capsid protein G8P
Y: Capsid protein G8P
Z: Capsid protein G8P
AA: Capsid protein G8P
BA: Capsid protein G8P
CA: Capsid protein G8P
DA: Capsid protein G8P
EA: Capsid protein G8P
FA: Capsid protein G8P
GA: Capsid protein G8P
HA: Capsid protein G8P
IA: Capsid protein G8P
JA: Capsid protein G8P
KA: Capsid protein G8P
LA: Capsid protein G8P
MA: Capsid protein G8P
NA: Capsid protein G8P
OA: Capsid protein G8P


Theoretical massNumber of molelcules
Total (without water)209,72140
Polymers209,72140
Non-polymers00
Water00
1


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

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Components

#1: Protein/peptide ...
Capsid protein G8P / Coat protein B / Gene 8 protein / G8P / M13 procoat / Major coat protein


Mass: 5243.014 Da / Num. of mol.: 40
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Inovirus M13 / Gene: VIII / Production host: Escherichia coli (E. coli) / References: UniProt: P69541

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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: middle 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 FIELD / 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 368282 / Symmetry type: POINT

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