9K09 | pdb_00009k09

Cyanophage A4 portal-tail complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Cryo-EM structure of cyanopodophage A4 reveals a pentameric pre-ejectosome in the double-stabilized capsid.

Hou, P.Zhou, R.Q.Jiang, Y.L.Yu, R.C.Du, K.Gan, N.Ke, F.Zhang, Q.Y.Li, Q.Zhou, C.Z.

(2025) Proc Natl Acad Sci U S A 122: e2423403122-e2423403122

  • DOI: https://doi.org/10.1073/pnas.2423403122
  • Primary Citation Related Structures: 
    9JWB, 9K09, 9K2V, 9K3A

  • PubMed Abstract: 

    Upon infection, the podophages usually eject a couple of proteins from the capsid to form a transmembrane ejectosome on the host cell membrane that facilitates the ejection of viral genome. However, it remains unclear how these proteins of pre-ejectosome are finely assembled at the center of highly packaged genome. Here, we report the intact structure of Anabaena cyanopodophage A4, which consists of a capsid stabilized by two types of cement proteins and a short tail attached with six tail fibers. Notably, we find a pentameric pre-ejectosome at the core of capsid, which is composed of four ejection proteins wrapped into a coaxial cylinder of triple layers. Moreover, a segment of genomic DNA runs along the positively charged circular cleft formed by two ejection proteins. Based on the mortise-and-tenon architecture of pre-ejectosome in combination with previous studies, we propose a putative DNA packaging process and ejection mechanism for podophages. These findings largely enrich our knowledge on the assembly mechanism of podophages, which might facilitate the application of A4 as a chassis cyanophage in synthetic biology.


  • Organizational Affiliation
    • Department of Radiology, The First Affiliated Hospital of University of Science and Technology of China and School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.

Macromolecule Content 

  • Total Structure Weight: 2,586.52 kDa 
  • Atom Count: 173,160 
  • Modeled Residue Count: 21,978 
  • Deposited Residue Count: 23,226 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tail fiber protein372Anabaena phage A-4LMutation(s): 0 
UniProt
Find proteins for A0A059PY41 (Anabaena phage A-4L)
Explore A0A059PY41 
Go to UniProtKB:  A0A059PY41
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059PY41
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Portal protein
D, E, F, G, H
D, E, F, G, H, I, J, K, L, M, N, O
653Anabaena phage A-4LMutation(s): 0 
UniProt
Find proteins for A0A059PYA9 (Anabaena phage A-4L)
Explore A0A059PYA9 
Go to UniProtKB:  A0A059PYA9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059PYA9
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Tail tubular protein B1,015Anabaena phage A-4LMutation(s): 0 
UniProt
Find proteins for A0A059PYE2 (Anabaena phage A-4L)
Explore A0A059PYE2 
Go to UniProtKB:  A0A059PYE2
Entity Groups
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UniProt GroupA0A059PYE2
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Tail tubular protein A217Anabaena phage A-4LMutation(s): 0 
UniProt
Find proteins for A0A059PY25 (Anabaena phage A-4L)
Explore A0A059PY25 
Go to UniProtKB:  A0A059PY25
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059PY25
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)ChinaU19A2020

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release