Related Experiment Video
Updated: Sep 18, 2025
09:03
Functional Imaging of Viral Transcription Factories Using 3D Fluorescence Microscopy
Published on: January 18, 2018
7.1K
Structure Prediction of Complexes Controlling Beta- and Gamma-Herpesvirus Late Transcription Using AlphaFold 3
1Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA 52240, USA.
Viruses
|June 27, 2025
Summary
This study used AlphaFold3 to predict the structure of late transcription factor complexes in herpesviruses. The predicted structures reveal conserved features and provide insights into viral transcription regulation.
Area of Science:
- Virology
- Structural Biology
- Molecular Biology
Background:
- Beta- and gamma-herpesviruses employ six viral proteins forming a complex to regulate late-life cycle transcription.
- This complex binds TA-rich sequences upstream of late transcription start sites, recruiting RNA polymerase II (Pol II).
- Prior structural data for these late transcription factors (LTFs) and their complexes were limited.
Purpose of the Study:
- To predict and analyze the structure of the LTF complex across various beta- and gamma-herpesviruses using AlphaFold3.
- To investigate the structural conservation and functional implications of the LTF complex.
Main Methods:
- Utilized AlphaFold3 for structure prediction of LTF complexes from human cytomegalovirus (HCMV), murine cytomegalovirus (MCMV), human herpesvirus 6 (HHV6), human herpesvirus 7 (HHV7), Epstein-Barr virus (EBV), and Kaposi's sarcoma-associated herpesvirus (KSHV).
- Analyzed predicted structures for confidence levels, similarity across viral families, and conservation of key functional sites.
Main Results:
- AlphaFold3 generated high-confidence structural predictions for LTF complexes, showing remarkable similarity despite low sequence conservation among LTFs.
- Predicted structures align with existing knowledge of LTF interactions with each other and DNA.
- Identified a conserved threonine phosphorylation site at a critical junction and predicted multiple metal ion binding sites within the complexes.
Conclusions:
- The conserved structural features of LTF complexes across diverse herpesviruses suggest a conserved mechanism for regulating viral transcription.
- Predicted structures offer novel insights into LTF function, subunit interactions, and potential interactions with host general transcription factors (GTFs).
- AlphaFold3 proves valuable for elucidating the structure and function of viral protein complexes.
More Related Videos
08:26Purification of Viral DNA for the Identification of Associated Viral and Cellular Proteins
Published on: August 31, 2017
13.8K
08:04Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
Published on: June 6, 2025
529
Related Concept Videos
02:28Leaky Scanning
5.2K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.2K
02:41Protein Complex Assembly
11.0K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Many viruses self-assemble into a fully functional unit using the infected host cell to...
11.0K
01:26Size and Structure of Viral Genomes
162
Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
162
01:49Conserved Binding Sites
4.4K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.4K
01:25Nucleic Acid Structure
7.2K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
DNA Structure
DNA...
7.2K