Capsid Structure of Anabaena Cyanophage A-1(L)

2021 ◽  
Author(s):  
Ning Cui ◽  
Feng Yang ◽  
Jun-Tao Zhang ◽  
Hui Sun ◽  
Yu Chen ◽  
...  
Keyword(s):  
Aquatic Ecosystems ◽  
Photosynthetic Bacteria ◽  
Atomic Resolution ◽  
Fold Axis ◽  
Contractile Tail ◽  
Phage Capsid ◽  
Mortise And Tenon ◽  
Pcc 7120 ◽  
Icosahedral Capsid ◽  
Resolution Structure

A-1(L) is a freshwater cyanophage with a contractile tail that specifically infects Anabaena sp. PCC 7120, one of the model strains for molecular studies of cyanobacteria. Although isolated for half a century, its structure remains unknown, which limits our understanding on the interplay between A-1(L) and its host. Here we report the 3.35 Å cryo-EM structure of A-1(L) capsid, representing the first near-atomic resolution structure of a phage capsid with a T number of 9. The major capsid gp4 proteins assemble into 91 capsomers, including 80 hexons: 20 at the center of the facet and 60 at the facet edge, in addition to 11 identical pentons. These capsomers further assemble into the icosahedral capsid, via gradually increasing curvatures. Different from the previously reported capsids of known-structure, A-1(L) adopts a non-covalent chainmail structure of capsid stabilized by two kinds of mortise-and-tenon inter-capsomer interactions: a three-layered interface at the pseudo three-fold axis combined with the complementarity in shape and electrostatic potential around the two-fold axis. This unique capsomer construction enables A-1(L) to possess a rigid capsid, which is solely composed of the major capsid proteins with an HK97 fold. IMPORTANCE Cyanobacteria are the most abundant photosynthetic bacteria, contributing significantly to the biomass production, O 2 generation, and CO 2 consumption on our planet. Their community structure and homeostasis in natural aquatic ecosystems are largely regulated by the corresponding cyanophages. In this study, we solved the structure of cyanophage A-1(L) capsid at near-atomic resolution and revealed a unique capsid construction. This capsid structure provides the molecular details for better understanding the assembly of A-1(L), and a structural platform for future investigation and application of A-1(L) in combination with its host Anabaena sp. PCC 7120. As the first isolated freshwater cyanophage that infects the genetically tractable model cyanobacterium, A-1(L) should become an ideal template for the genetic engineering and synthetic biology studies.

scholarly journals Structural Analysis of Jumbo Coliphage phAPEC6

2020 ◽  
Vol 21 (9) ◽  
pp. 3119 ◽  
Author(s):  
Jeroen Wagemans ◽  
Jessica Tsonos ◽  
Dominique Holtappels ◽  
Kiandro Fortuna ◽  
Jean-Pierre Hernalsteens ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Capsid Protein ◽  
Tem Analysis ◽  
Host Interaction ◽  
Cryo Electron Microscopy ◽  
Transmission Electron ◽  
Tail Sheath ◽  
Associated Proteins ◽  
Contractile Tail ◽  
Phage Capsid

The phAPEC6 genome encodes 551 predicted gene products, with the vast majority (83%) of unknown function. Of these, 62 have been identified as virion-associated proteins by mass spectrometry (ESI-MS/MS), including the major capsid protein (Gp225; present in 1620 copies), which shows a HK97 capsid protein-based fold. Cryo-electron microscopy experiments showed that the 350-kbp DNA molecule of Escherichia coli virus phAPEC6 is packaged in at least 15 concentric layers in the phage capsid. A capsid inner body rod is also present, measuring about 91 nm by 18 nm and oriented along the portal axis. In the phAPEC6 contractile tail, 25 hexameric stacked rings can be distinguished, built of the identified tail sheath protein (Gp277). Cryo-EM reconstruction reveals the base of the unique hairy fibers observed during an initial transmission electron microscopy (TEM) analysis. These very unusual filaments are ordered at three annular positions along the contractile sheath, as well as around the capsid, and may be involved in host interaction.

scholarly journals CryoEM structure of the antibacterial target PBP1b at 3.3 Å resolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nathanael A. Caveney ◽  
Sean D. Workman ◽  
Rui Yan ◽  
Claire E. Atkinson ◽  
Zhiheng Yu ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Acid Anhydride ◽  
Atomic Resolution ◽  
Inherent Difficulty ◽  
Penicillin Binding Proteins ◽  
Antibiotic Development ◽  
Class A ◽  
Membrane Mimetic ◽  
Antibacterial Target ◽  
Resolution Structure

AbstractThe pathway for the biosynthesis of the bacterial cell wall is one of the most prolific antibiotic targets, exemplified by the widespread use of β-lactam antibiotics. Despite this, our structural understanding of class A penicillin binding proteins, which perform the last two steps in this pathway, is incomplete due to the inherent difficulty in their crystallization and the complexity of their substrates. Here, we determine the near atomic resolution structure of the 83 kDa class A PBP from Escherichia coli, PBP1b, using cryogenic electron microscopy and a styrene maleic acid anhydride membrane mimetic. PBP1b, in its apo form, is seen to exhibit a distinct conformation in comparison to Moenomycin-bound crystal structures. The work herein paves the way for the use of cryoEM in structure-guided antibiotic development for this notoriously difficult to crystalize class of proteins and their complex substrates.

scholarly journals A resolution record for cryoEM

2021 ◽  
Vol 10 ◽  
Author(s):  
Jonathan Ashmore ◽  
Bridget Carragher ◽  
Peter B Rosenthal ◽  
William Weis
Keyword(s):  
Electron Microscopy ◽  
Image Analysis ◽  
Structure Determination ◽  
Test Specimen ◽  
Structural Information ◽  
Atomic Resolution ◽  
Fast Growing ◽  
Cryo Electron Microscopy ◽  
New Instrument ◽  
Resolution Structure

Cryo electron microscopy (cryoEM) is a fast-growing technique for structure determination. Two recent papers report the first atomic resolution structure of a protein obtained by averaging images of frozen-hydrated biomolecules. They both describe maps of symmetric apoferritin assemblies, a common test specimen, in unprecedented detail. New instrument improvements, different in the two studies, have contributed better images, and image analysis can extract structural information sufficient to resolve individual atomic positions. While true atomic resolution maps will not be routine for most proteins, the studies suggest structures determined by cryoEM will continue to improve, increasing their impact on biology and medicine.

A Covalent Modification of NADP+Revealed by the Atomic Resolution Structure of FprA, aMycobacterium tuberculosisOxidoreductase†,‡

Biochemistry ◽  
2002 ◽  
Vol 41 (28) ◽  
pp. 8807-8818 ◽  
Author(s):  
Roberto T. Bossi ◽  
Alessandro Aliverti ◽  
Debora Raimondi ◽  
Federico Fischer ◽  
Giuliana Zanetti ◽  
...  
Keyword(s):  
Covalent Modification ◽  
Atomic Resolution ◽  
Resolution Structure

scholarly journals Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR

2015 ◽  
Vol 1 (11) ◽  
pp. e1501087 ◽  
Author(s):  
Chaowei Shi ◽  
Pascal Fricke ◽  
Lin Lin ◽  
Veniamin Chevelkov ◽  
Melanie Wegstroth ◽  
...  
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Caulobacter Crescentus ◽  
Heavy Atom ◽  
Cytoskeletal Proteins ◽  
Atomic Resolution ◽  
Hydrophobic Core ◽  
X Ray Crystallography ◽  
Wide Range ◽  
Resolution Structure

Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the speciesCaulobacter crescentusis not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR–derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.

Atomic Resolution Structure of Human HBP/CAP37/Azurocidin

1998 ◽  
Vol 54 (4) ◽  
pp. 598-609 ◽  
Author(s):  
Solveig Karlsen ◽  
Lars Fogh Iversen ◽  
Ingrid Kjøller Larsen ◽  
Hans Jacob Flodgaard ◽  
Jette Sandholm Kastrup
Keyword(s):  
Atomic Resolution ◽  
Resolution Structure

scholarly journals Atomic-resolution structure of the  -galactosyl binding Lyophyllum decastes lectin reveals a new protein family found in both fungi and plants

Glycobiology ◽  
2014 ◽  
Vol 25 (5) ◽  
pp. 492-501 ◽  
Author(s):  
A. van Eerde ◽  
E. M. Grahn ◽  
H. C. Winter ◽  
I. J. Goldstein ◽  
U. Krengel
Keyword(s):  
Protein Family ◽  
Atomic Resolution ◽  
New Protein ◽  
Lyophyllum Decastes ◽  
Resolution Structure

scholarly journals The Missing Tailed Phages: Prediction of Small Capsid Candidates

2020 ◽  
Vol 8 (12) ◽  
pp. 1944
Author(s):  
Antoni Luque ◽  
Sean Benler ◽  
Diana Y. Lee ◽  
Colin Brown ◽  
Simon White
Keyword(s):  
Phage Therapy ◽  
Viral Evolution ◽  
Diverse Group ◽  
Genome Length ◽  
Geometrical Features ◽  
Phage Capsid ◽  
The Common ◽  
Icosahedral Capsid ◽  
Gut Metagenome ◽  
Physical Principles

Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common icosahedral capsid architectures T = 1 and T = 3 is puzzling. Here, we extracted geometrical features from high-resolution tailed phage capsid reconstructions and built a statistical model based on physical principles to predict the capsid diameter and genome length of the missing small-tailed phage capsids. We applied the model to 3348 isolated tailed phage genomes and 1496 gut metagenome-assembled tailed phage genomes. Four isolated tailed phages were predicted to form T = 3 icosahedral capsids, and twenty-one metagenome-assembled tailed phages were predicted to form T < 3 capsids. The smallest capsid predicted was a T = 4/3 ≈ 1.33 architecture. No tailed phages were predicted to form the smallest icosahedral architecture, T = 1. We discuss the feasibility of the missing T = 1 tailed phage capsids and the implications of isolating and characterizing small-tailed phages for viral evolution and phage therapy.

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