4.8 Article

Structural basis for the inactivation of cytosolic DNA sensing by the vaccinia virus

Related references

Note: Only part of the references are listed.
Review Biochemistry & Molecular Biology

Nuclear antiviral innate responses at the intersection of DNA sensing and DNA repair

Joshua L. Justice et al.

Summary: The coevolution of vertebrate and mammalian hosts with DNA viruses has led to the development of host cell abilities to differentiate viral and cellular DNA, triggering innate immune responses. This interaction has also resulted in viral mechanisms to inhibit DNA sensing. Within this virus-host interface, there is evidence linking cytokine responses and cellular homeostasis pathways, specifically the DNA damage response (DDR). Nuclear DNA sensors such as interferon (IFN)-gamma inducible protein 16 (IFI16) intersect with the DDR regulators ataxia telangiectasia mutated (ATM) and DNA-dependent protein kinase (DNA-PK). In this article, we discuss the accumulating knowledge regarding the DDR-innate immunity signaling axis and present acquired host and viral molecular strategies to regulate autoinflammation and antiviral responses.

TRENDS IN MICROBIOLOGY (2022)

Article Biology

DeepEMhancer: a deep learning solution for cryo-EM volume post-processing

Ruben Sanchez-Garcia et al.

Summary: Sanchez-Garcia et al. introduce DeepEMhancer, a deep learning-based method for automatic post-processing of raw cryo-electron microscopy density maps. It globally improves local quality of density maps and shows potential as a useful tool for structures without readily available PDB models.

COMMUNICATIONS BIOLOGY (2021)

Article Biochemistry & Molecular Biology

New tools for automated cryo-EM single-particle analysis in RELION-4.0

Dari Kimanius et al.

Summary: This article introduces new tools for processing cryo-EM images in the fourth major release of the RELION software, including VDAM algorithm, convolutional neural network, and a framework for executing multiple jobs, along with a utility called MDCatch for metadata gathering during microscope data acquisition. These tools aim to provide fast and robust procedures for unsupervised cryo-EM structure determination, with potential applications for on-the-fly processing and flexible, high-throughput structure determination pipelines.

BIOCHEMICAL JOURNAL (2021)

Article Biochemistry & Molecular Biology

Structure of an activated DNA-PK and its implications for NHEJ

Xuemin Chen et al.

Summary: This study reports cryo-EM structures of DNA-PK in both inactive and activated forms bound to DNA end or complexed with Ku70/80 and DNA, revealing the sequential transition of DNA-PK from inactive to activated forms. Activation of the kinase involves unprecedented stretching and twisting within individual solenoid segments, indicating a general regulatory mechanism of HEAT-repeat proteins.

MOLECULAR CELL (2021)

Article Biochemistry & Molecular Biology

SAP domain forms a flexible part of DNA aperture in Ku70/80

Ales Hnizda et al.

Summary: Nonhomologous end joining (NHEJ) is a DNA repair mechanism that maintains genomic integrity, with the Ku70/80 complex playing a critical role in recognizing DNA breaks. Research has shown that the SAP domain in the Ku70 C-terminal region changes its position depending on DNA binding, potentially serving as a flexible entry gate for broken DNA.

FEBS JOURNAL (2021)

Review Immunology

The Role of Ku70 as a Cytosolic DNA Sensor in Innate Immunity and Beyond

Hongyan Sui et al.

Summary: Ku70, known for its role in DNA repair, has been identified as a multifunctional protein involved in various cellular processes. This review focuses on its role as a cytosolic DNA sensor, inducing interferons and proinflammatory cytokines, and discusses the unique structure of Ku70 binding with DNA and its involvement in the innate immune response pathway. Strategies to modulate Ku70-mediated innate immune response are also discussed, along with potential physiological insights based on its role in innate immunity.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2021)

Article Multidisciplinary Sciences

Structural basis of long-range to short-range synaptic transition in NHEJ

Siyu Chen et al.

Summary: In this study, single-particle cryo-electron microscopy was used to visualize two key DNA-protein complexes formed by human NHEJ factors, revealing their structure and interactions.

NATURE (2021)

Article Biochemistry & Molecular Biology

3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM

Ali Punjani et al.

Summary: 3DVA is an algorithm that fits a linear subspace model of conformational change to high-resolution cryo-EM data, enabling the resolution and visualization of detailed molecular motions of proteins. It has been shown to successfully resolve multiple flexible motions in various protein complexes, providing new biological insights from single particle cryo-EM data.

JOURNAL OF STRUCTURAL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Cryo-EM of NHEJ supercomplexes provides insights into DNA repair

Amanda K. Chaplin et al.

Summary: Non-homologous end joining (NHEJ) is a critical mechanism for repairing DNA double-strand breaks in humans, involving core proteins such as Ku70/80 heterodimer. Cryo-EM structures of NHEJ supercomplexes reveal detailed structural assembly and mutational disruption of these complexes negatively affects DNA repair.

MOLECULAR CELL (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Review Physiology

DNA Sensing in the Innate Immune Response

Benoit Briard et al.

PHYSIOLOGY (2020)

Article Immunology

Human DNA-PK activates a STING-independent DNA sensing pathway

Katelyn Burleigh et al.

SCIENCE IMMUNOLOGY (2020)

Review Biotechnology & Applied Microbiology

Viral interactions with non-homologous end -joining: a game of hide-and-seek

Dayana B. Hristova et al.

JOURNAL OF GENERAL VIROLOGY (2020)

Review Immunology

Vaccinia Virus Activation and Antagonism of Cytosolic DNA Sensing

Misbah El-Jesr et al.

FRONTIERS IN IMMUNOLOGY (2020)

Review Immunology

Molecular and Structural Basis of DNA Sensors in Antiviral Innate Immunity

Ayesha Zahid et al.

FRONTIERS IN IMMUNOLOGY (2020)

Article Multidisciplinary Sciences

Viral and metazoan poxins are cGAMP-specific nucleases that restrict cGAS-STING signalling

James B. Eaglesham et al.

NATURE (2019)

Article Biochemical Research Methods

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

Tristan Bepler et al.

NATURE METHODS (2019)

Article Biochemical Research Methods

Real-space refinement in PHENIX for cryo-EM and crystallography

Pavel V. Afonine et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2018)

Article Cell Biology

DNA-PK Is Targeted by Multiple Vaccinia Virus Proteins to Inhibit DNA Sensing

Simon R. Scutts et al.

CELL REPORTS (2018)

Letter Biochemical Research Methods

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

Shawn Q. Zheng et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

Ali Punjani et al.

NATURE METHODS (2017)

Article Cell Biology

Cryo-EM structure of human DNA-PK holoenzyme

Xiaotong Yin et al.

CELL RESEARCH (2017)

Article Biochemistry & Molecular Biology

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

Alexis Rohou et al.

JOURNAL OF STRUCTURAL BIOLOGY (2015)

Article Biotechnology & Applied Microbiology

A role for vaccinia virus protein C16 in reprogramming cellular energy metabolism

Michela Mazzon et al.

JOURNAL OF GENERAL VIROLOGY (2015)

Article Biochemistry & Molecular Biology

APLF promotes the assembly and activity of non-homologous end joining protein complexes

Gabrielle J. Grundy et al.

EMBO JOURNAL (2013)

Article Multidisciplinary Sciences

A mechanism for induction of a hypoxic response by vaccinia virus

Michela Mazzon et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Microbiology

A Mechanism for the Inhibition of DNA-PK-Mediated DNA Sensing by a Virus

Nicholas E. Peters et al.

PLOS PATHOGENS (2013)

Editorial Material Microbiology

Viruses, Masters at Downsizing

Daniel DiMaio

CELL HOST & MICROBE (2012)

Article Biotechnology & Applied Microbiology

Vaccinia virus protein C4 inhibits NF-κB activation and promotes virus virulence

Stuart W. J. Ember et al.

JOURNAL OF GENERAL VIROLOGY (2012)

Article Biology

DNA-PK is a DNA sensor for IRF-3-dependent innate immunity

Brian J. Ferguson et al.

ELIFE (2012)

Article Biochemical Research Methods

Features and development of Coot

P. Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemistry & Molecular Biology

The bridge-region of the Ku superfamily is an atypical zinc ribbon domain

S. Sri Krishna et al.

JOURNAL OF STRUCTURAL BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

Vaccinia virus protein C16 acts intracellularly to modulate the host response and promote virulence

Aodhnait S. Fahy et al.

JOURNAL OF GENERAL VIROLOGY (2008)

Article Multidisciplinary Sciences

Cellular oxygen sensing:: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)

Michael A. McDonough et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemical Research Methods

RF cloning:: A restriction-free method for inserting target genes into plasmids

F van den Ent et al.

JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS (2006)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Biochemistry & Molecular Biology

Poxviruses and the origin of the eukaryotic nucleus

M Takemura

JOURNAL OF MOLECULAR EVOLUTION (2001)

Article Biochemistry & Molecular Biology

T-Coffee: A novel method for fast and accurate multiple sequence alignment

C Notredame et al.

JOURNAL OF MOLECULAR BIOLOGY (2000)