2XD8 | pdb_00002xd8

Capsid structure of the infectious Prochlorococcus Cyanophage P-SSP7

• PDB DOI: https://doi.org/10.2210/pdb2XD8/pdb
• EM Map EMD-1713: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Tiamatvirus PSSP7
• Expression System: Prochlorococcus sp.
• Mutation(s): No 


• Deposited: 2010-04-30 Released: 2010-06-16 
• Deposition Author(s): Liu, X., Zhang, Q., Murata, K., Baker, M.L., Sullivan, M.B., Fu, C., Dougherty, M., Schmid, M.F., Osburne, M.S., Chisholm, S.W., Chiu, W.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Structural Changes in a Marine Podovirus Associated with Release of its Genome Into Prochlorococcus

Liu, X., Zhang, Q., Murata, K., Baker, M.L., Sullivan, M.B., Fu, C., Dougherty, M., Schmid, M.F., Osburne, M.S., Chisholm, S.W., Chiu, W.

(2010) Nat Struct Mol Biol 17: 830

• PubMed: 20543830 
• DOI: https://doi.org/10.1038/nsmb.1823
• Primary Citation Related Structures: 
  2XD8


• PubMed Abstract: 
  

  Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic photosynthetic microorganism. Single-particle cryo-electron microscopy yields icosahedral and asymmetrical structures of infectious P-SSP7 with 4.6-A and 9-A resolution, respectively. The asymmetric reconstruction reveals how symmetry mismatches are accommodated among five of the gene products at the portal vertex. Reconstructions of infectious and empty particles show a conformational change of the 'valve' density in the nozzle, an orientation difference in the tail fibers, a disordering of the C terminus of the portal protein and the disappearance of the core proteins. In addition, cryo-electron tomography of P-SSP7 infecting Prochlorococcus showed the same tail-fiber conformation as that in empty particles. Our observations suggest a mechanism whereby, upon binding to the host cell, the tail fibers induce a cascade of structural alterations of the portal vertex complex that triggers DNA release.

---

Organizational Affiliation: 
• National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 420-mer - A420 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 276.46 kDa 
• Atom Count: 2,541 
• Modeled Residue Count: 2,541 
• Deposited Residue Count: 2,625 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T7-LIKE CAPSID PROTEIN	A, B, C, D, E, F, G	375	Tiamatvirus PSSP7	Mutation(s): 0
UniProt
Find proteins for Q58N30 (Prochlorococcus phage P-SSP7) Explore Q58N30  Go to UniProtKB:  Q58N30

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	MPSA

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-16 
Deposition Author(s): Liu, X., Zhang, Q., Murata, K., Baker, M.L., Sullivan, M.B., Fu, C., Dougherty, M., Schmid, M.F., Osburne, M.S., Chisholm, S.W., Chiu, W.

Revision History  

• Version 1.0: 2010-06-16
  Type: Initial release
  
• Version 1.1: 2013-03-20
  Changes: Other, Refinement description, Version format compliance
• Version 1.2: 2018-10-03
  Changes: Data collection
• Version 1.3: 2019-10-23
  Changes: Data collection, Other
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Refinement description