8FQK | pdb_00008fqk

Asymmetric unit of HK97 phage prohead I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8FQK

This is version 1.1 of the entry. See complete history

Literature

A symmetry mismatch unraveled: How phage HK97 scaffold flexibly accommodates a 12-fold pore at a 5-fold viral capsid vertex.

Huet, A.Oh, B.Maurer, J.Duda, R.L.Conway, J.F.

(2023) Sci Adv 9: eadg8868-eadg8868

  • DOI: https://doi.org/10.1126/sciadv.adg8868
  • Primary Citation Related Structures: 
    8FQK, 8FQL

  • PubMed Abstract: 

    Tailed bacteriophages and herpesviruses use a transient scaffold to assemble icosahedral capsids with hexameric capsomers on the faces and pentameric capsomers at all but one vertex where a 12-fold portal is thought to nucleate the assembly. How does the scaffold orchestrate this step? We have determined the portal vertex structure of the bacteriophage HK97 procapsid, where the scaffold is a domain of the major capsid protein. The scaffold forms rigid helix-turn-strand structures on the interior surfaces of all capsomers and is further stabilized around the portal, forming trimeric coiled-coil towers, two per surrounding capsomer. These 10 towers bind identically to 10 of 12 portal subunits, adopting a pseudo-12-fold organization that explains how the symmetry mismatch is managed at this early step.


  • Organizational Affiliation
    • Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

Macromolecule Content 

  • Total Structure Weight: 296.01 kDa 
  • Atom Count: 14,593 
  • Modeled Residue Count: 1,873 
  • Deposited Residue Count: 2,695 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Scaffolding domain delta
A, B, C, D, E
A, B, C, D, E, F, G
385Escherichia phage HK97Mutation(s): 0 
UniProt
Find proteins for P49861 (Enterobacteria phage HK97)
Explore P49861 
Go to UniProtKB:  P49861
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49861
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTUCSF ChimeraX
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM144981
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM47795

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection