ArticleProceedings of the National Academy of Sciences of the United States of America2022
PTX3 structure determination using a hybrid cryoelectron microscopy and AlphaFold approach offers insights into ligand binding and complement activation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- Backbone resonance assignment of the pentraxin domain of the neuronal pentraxin receptor (NPTXR).Biomolecular NMR assignments · 2026Article
- Proteomic Analysis of Cerebrospinal Fluid: Toward the Identification of Biomarkers for Early Central Nervous System Infection.Infection and drug resistance · 2026Article
- Diagnostic value and challenges in the immune regulation of pentraxin 3 in infectious diseases.Frontiers in microbiology · 2026Review
- Resurgence of magnetic resonance techniques in the era of AlphaFold.Biophysical reviews · 2025Review
- Challenges in bridging the gap between protein structure prediction and functional interpretation.Proteins · 2025Article
- Navigating the unstructured by evaluating alphafold's efficacy in predicting missing residues and structural disorder in proteins.PloS one · 2025Article
- The long pentraxin 3: the invisible loom weaving the warp and weft of tumor destiny.Frontiers in immunology · 2025Review
- Soluble Human Lectins at the Host-Microbe Interface.Annual review of biochemistry · 2024Review
- Functional variants of the pentraxin 3 gene are associated with the metastasis and progression of prostate cancer.Journal of cellular and molecular medicine · 2024Article
- sMR and PTX3 levels associate with COVID-19 outcome and survival but not with Long COVID.iScience · 2024Article
- AlphaFold2 as a replacement for solution NMR structure determination of small proteins: Not so fast!Journal of magnetic resonance (San Diego, Calif. : 1997) · 2024Article
- Improved therapeutic consistency and efficacy of CD317Stem cell research & therapy · 2024Article
- Predictive modeling and cryo-EM: A synergistic approach to modeling macromolecular structure.Biophysical journal · 2024Review
- Genetic Deficiency of the Long Pentraxin 3 Affects Osteogenesis and Osteoclastogenesis in Homeostatic and Inflammatory Conditions.International journal of molecular sciences · 2023Article
- Long Pentraxin 3 as a New Biomarker for Diagnosis of Hip and Knee Periprosthetic Joint Infections.Journal of clinical medicine · 2023Article
- Structural insights into the biological functions of the long pentraxin PTX3.Frontiers in immunology · 2023Review
- Before and after AlphaFold2: An overview of protein structure prediction.Frontiers in bioinformatics · 2023Review
- PTX3 structure determination using a hybrid cryoelectron microscopy and AlphaFold approach offers insights into ligand binding and complement activation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pattern recognition molecules (PRMs) form an important part of innate immunity, where they facilitate the response to infections and damage by triggering processes such as inflammation. The pentraxin family of soluble PRMs comprises long and short pentraxins, with the former containing unique N-terminal regions unrelated to other proteins or each other. No complete high-resolution structural information exists about long pentraxins, unlike the short pentraxins, where there is an abundance of both X-ray and cryoelectron microscopy (cryo-EM)-derived structures. This study presents a high-resolution structure of the prototypical long pentraxin, PTX3. Cryo-EM yielded a 2.5-Å map of the C-terminal pentraxin domains that revealed a radically different quaternary structure compared to other pentraxins, comprising a glycosylated D4 symmetrical octameric complex stabilized by an extensive disulfide network. The cryo-EM map indicated α-helices that extended N terminal of the pentraxin domains that were not fully resolved. AlphaFold was used to predict the remaining N-terminal structure of the octameric PTX3 complex, revealing two long tetrameric coiled coils with two hinge regions, which was validated using classification of cryo-EM two-dimensional averages. The resulting hybrid cryo-EM/AlphaFold structure allowed mapping of ligand binding sites, such as C1q and fibroblast growth factor-2, as well as rationalization of previous biochemical data. Given the relevance of PTX3 in conditions ranging from COVID-19 prognosis, cancer progression, and female infertility, this structure could be used to inform the understanding and rational design of therapies for these disorders and processes.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.