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- PDB-8jwt: Asymmetric middle segment of the bacteriophage M13 mini variant -

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Basic information

Entry
Database: PDB / ID: 8jwt
TitleAsymmetric middle segment of the bacteriophage M13 mini variant
ComponentsCapsid protein G8P
KeywordsVIRAL 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 speciesEnterobacteria phage M13 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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
DepositionJun 29, 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
Revision 1.2Jul 23, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Capsid protein G8P
G: Capsid protein G8P
H: Capsid protein G8P
I: Capsid protein G8P
J: Capsid protein G8P
E: Capsid protein G8P
D: Capsid protein G8P
Q: Capsid protein G8P
A: Capsid protein G8P
B: Capsid protein G8P
C: Capsid protein G8P
K: Capsid protein G8P
L: Capsid protein G8P
M: Capsid protein G8P
N: Capsid protein G8P
O: Capsid protein G8P
P: 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&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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.) Enterobacteria phage M13 (virus) / Gene: VIII / Production host: Escherichia (bacteria) / References: UniProt: P69541
Has protein modificationN

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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: Asymmetric middle segment of the bacteriophage M13 mini variant
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Enterobacteria phage M13 (virus)
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

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 278052 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314040
ELECTRON MICROSCOPYf_angle_d0.38319000
ELECTRON MICROSCOPYf_dihedral_angle_d3.1461920
ELECTRON MICROSCOPYf_chiral_restr0.0332240
ELECTRON MICROSCOPYf_plane_restr0.0022280

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