National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM144981
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM47795
United States
Citation
Journal: Sci Adv / Year: 2023 Title: A symmetry mismatch unraveled: How phage HK97 scaffold flexibly accommodates a 12-fold pore at a 5-fold viral capsid vertex. Authors: Alexis Huet / Bonnie Oh / Josh Maurer / Robert L Duda / James F Conway / 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 ...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.
History
Deposition
Jan 6, 2023
Deposition site: RCSB / Processing site: RCSB
Revision 1.0
Jun 28, 2023
Provider: repository / Type: Initial release
Revision 1.1
Jun 19, 2024
Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2909
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Processing
EM software
ID
Name
Category
1
EMAN2
particleselection
2
EPU
imageacquisition
4
CTFFIND
CTFcorrection
7
UCSF Chimera
modelfitting
9
RELION
initialEulerassignment
10
RELION
finalEulerassignment
12
RELION
3Dreconstruction
13
UCSF ChimeraX
modelrefinement
14
PHENIX
modelrefinement
15
Coot
modelrefinement
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Symmetry
Point symmetry: I (icosahedral)
3D reconstruction
Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72945 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model building
Protocol: FLEXIBLE FIT / Space: REAL
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