+Open data
-Basic information
Entry | Database: PDB / ID: 7zl1 | ||||||
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Title | PTX3 Pentraxin Domain | ||||||
Components | Pentraxin-related protein PTX3 | ||||||
Keywords | IMMUNE SYSTEM / PTX3 / Long pentraxin 3 / innate immunity | ||||||
Function / homology | Function and homology information (1->3)-beta-D-glucan binding / negative regulation by host of viral exo-alpha-sialidase activity / negative regulation by host of viral glycoprotein metabolic process / negative regulation of exo-alpha-sialidase activity / negative regulation of glycoprotein metabolic process / ovarian cumulus expansion / negative regulation by host of viral process / opsonization / complement component C1q complex binding / response to yeast ...(1->3)-beta-D-glucan binding / negative regulation by host of viral exo-alpha-sialidase activity / negative regulation by host of viral glycoprotein metabolic process / negative regulation of exo-alpha-sialidase activity / negative regulation of glycoprotein metabolic process / ovarian cumulus expansion / negative regulation by host of viral process / opsonization / complement component C1q complex binding / response to yeast / negative regulation of viral entry into host cell / virion binding / positive regulation of phagocytosis / extracellular matrix organization / extracellular matrix / specific granule lumen / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / inflammatory response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||
Authors | Noone, D.P. / Sharp, T.H. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: PTX3 structure determination using a hybrid cryoelectron microscopy and AlphaFold approach offers insights into ligand binding and complement activation. Authors: Dylan P Noone / Douwe J Dijkstra / Teun T van der Klugt / Peter A van Veelen / Arnoud H de Ru / Paul J Hensbergen / Leendert A Trouw / Thomas H Sharp / 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 ...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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zl1.cif.gz | 646 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zl1.ent.gz | 541.3 KB | Display | PDB format |
PDBx/mmJSON format | 7zl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zl1_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7zl1_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7zl1_validation.xml.gz | 61.1 KB | Display | |
Data in CIF | 7zl1_validation.cif.gz | 84.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/7zl1 ftp://data.pdbj.org/pub/pdb/validation_reports/zl/7zl1 | HTTPS FTP |
-Related structure data
Related structure data | 14774MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 41842.914 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: Pentraxin domain of the long pentraxin 3. No N-terminal domain is included in this coordinate file. Source: (gene. exp.) Homo sapiens (human) / Gene: PTX3, TNFAIP5, TSG14 / Production host: Homo sapiens (human) / References: UniProt: P26022 #2: Sugar | ChemComp-NAG / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Long pentraxin 3 pentraxin domain / Type: COMPLEX Details: CryoEM derived map of the pentraxin domains of PTX3. At higher isosurface threshold values the start of the coiled coil N-terminal domain can be seen. Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.336 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 23 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: PTX3 at concentrations between 1-2 uM in 20 mM Tris-HCl, 500 mM NaCl, pH 8.0 was concentrated in a 50 kDa molecular weight cut-off spin filter to concentrations between 60-70 uM. | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 65 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 103.15 K / Temperature (min): 90.15 K |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4612 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1360284 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D4 (2x4 fold dihedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 276374 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
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