9OCB | pdb_00009ocb

Sf11 capsid Icosahedral Reconstruction

• PDB DOI: https://doi.org/10.2210/pdb9OCB/pdb
• EM Map EMD-70309: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Shigella phage Sf11 SMD-2017
• Mutation(s): No 


• Deposited: 2025-04-24 Released: 2025-11-12 
• Deposition Author(s): Subramanian, S., Parent, K.N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of Shigella bacteriophage Sf11

Subramanian, S., Dover, J.A., Parent, K.N.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 840-mer - A420B420 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 389.2 kDa 
• Atom Count: 24,504 
• Modeled Residue Count: 3,211 
• Deposited Residue Count: 3,577 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein gp39	A, B, C, D, E, F, G	356	Shigella phage Sf11 SMD-2017	Mutation(s): 0
UniProt
Find proteins for A0A291AXD4 (Shigella phage Sf11 SMD-2017) Explore A0A291AXD4  Go to UniProtKB:  A0A291AXD4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative capsid decoration protein gp40	H, I, J, K, L, M, N	155	Shigella phage Sf11 SMD-2017	Mutation(s): 0
UniProt
Find proteins for A0A291AXD6 (Shigella phage Sf11 SMD-2017) Explore A0A291AXD6  Go to UniProtKB:  A0A291AXD6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Subramanian, S., Parent, K.N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM116789
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM140803
National Science Foundation (NSF, United States)	United States	1750125

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release