8IXK | pdb_00008ixk

bottom segment of the bacteriophage M13 mini variant

  • Classification: VIRAL PROTEIN
  • Organism(s): Inovirus M13
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-04-01 Released: 2023-09-13 
  • Deposition Author(s): Xiang, Y., Jia, Q.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8IXK

This is version 1.1 of the entry. See complete history

Literature

Cryo-EM structure of a bacteriophage M13 mini variant.

Jia, Q.Xiang, Y.

(2023) Nat Commun 14: 5421-5421

  • DOI: https://doi.org/10.1038/s41467-023-41151-7
  • Primary Citation Related Structures: 
    8IXJ, 8IXK, 8IXL, 8JWT

  • PubMed 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 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.


  • Organizational Affiliation
    • Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, P.R. China.

Macromolecule Content 

  • Total Structure Weight: 389.15 kDa 
  • Atom Count: 14,790 
  • Modeled Residue Count: 1,950 
  • Deposited Residue Count: 3,685 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Attachment protein G3PA [auth R],
F [auth A],
K [auth F],
P [auth K],
U [auth T]
406Inovirus M13Mutation(s): 0 
Gene Names: III
UniProt
Find proteins for P69168 (Enterobacteria phage M13)
Explore P69168 
Go to UniProtKB:  P69168
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69168
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein G8P73Inovirus M13Mutation(s): 0 
Gene Names: VIII
UniProt
Find proteins for P69541 (Enterobacteria phage M13)
Explore P69541 
Go to UniProtKB:  P69541
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69541
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Head virion protein G6PE [auth Z],
J [auth E],
O [auth J],
T [auth O],
Y
112Inovirus M13Mutation(s): 0 
Gene Names: VI
UniProt
Find proteins for P69532 (Enterobacteria phage M13)
Explore P69532 
Go to UniProtKB:  P69532
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69532
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Database references