9OCB | pdb_00009ocb

Sf11 capsid Icosahedral Reconstruction

  • 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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9OCB

This is version 1.0 of the entry. See complete history. 

Literature

Structure of Shigella bacteriophage Sf11

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

To be published.

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

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Major capsid protein gp39
A, B, C, D, E
A, B, C, D, E, F, G
356Shigella phage Sf11 SMD-2017Mutation(s): 0 
UniProt
Find proteins for A0A291AXD4 (Shigella phage Sf11 SMD-2017)
Explore A0A291AXD4 
Go to UniProtKB:  A0A291AXD4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A291AXD4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative capsid decoration protein gp40
H, I, J, K, L
H, I, J, K, L, M, N
155Shigella phage Sf11 SMD-2017Mutation(s): 0 
UniProt
Find proteins for A0A291AXD6 (Shigella phage Sf11 SMD-2017)
Explore A0A291AXD6 
Go to UniProtKB:  A0A291AXD6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A291AXD6
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM116789
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM140803
National Science Foundation (NSF, United States)United States1750125

Revision History  (Full details and data files)

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