+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42815 | |||||||||
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Title | PNMA2 capsid, focussed refinement of a pentamer (C5 symmetry) | |||||||||
Map data | Focussed refinement of PNMA2 capsid penton, C5 symmetry | |||||||||
Sample |
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Keywords | capsid / endogenous retrovirus-like particle / paraneoplasm / antigen / VIRUS LIKE PARTICLE | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||
Authors | Wilkinson ME / Madigan V / Zhang Y / Zhang F | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Human paraneoplastic antigen Ma2 (PNMA2) forms icosahedral capsids that can be engineered for mRNA delivery. Authors: Victoria Madigan / Yugang Zhang / Rumya Raghavan / Max E Wilkinson / Guilhem Faure / Elena Puccio / Michael Segel / Blake Lash / Rhiannon K Macrae / Feng Zhang / Abstract: A number of endogenous genes in the human genome encode retroviral -like proteins, which were domesticated from ancient retroelements. The paraneoplastic Ma antigen (PNMA) family members encode a - ...A number of endogenous genes in the human genome encode retroviral -like proteins, which were domesticated from ancient retroelements. The paraneoplastic Ma antigen (PNMA) family members encode a -like capsid domain, but their ability to assemble as capsids and traffic between cells remains mostly uncharacterized. Here, we systematically investigate human PNMA proteins and find that a number of PNMAs are secreted by human cells. We determine that PNMA2 forms icosahedral capsids efficiently but does not naturally encapsidate nucleic acids. We resolve the cryoelectron microscopy (cryo-EM) structure of PNMA2 and leverage the structure to design engineered PNMA2 (ePNMA2) particles with RNA packaging abilities. Recombinantly purified ePNMA2 proteins package mRNA molecules into icosahedral capsids and can function as delivery vehicles in mammalian cell lines, demonstrating the potential for engineered endogenous capsids as a nucleic acid therapy delivery modality. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42815.map.gz | 49.3 MB | EMDB map data format | |
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Header (meta data) | emd-42815-v30.xml emd-42815.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42815_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_42815.png | 195.2 KB | ||
Masks | emd_42815_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-42815.cif.gz | 4.5 KB | ||
Others | emd_42815_half_map_1.map.gz emd_42815_half_map_2.map.gz | 40.2 MB 40.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42815 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42815 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42815.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Focussed refinement of PNMA2 capsid penton, C5 symmetry | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.9654 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_42815_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Refinement half-map 1
File | emd_42815_half_map_1.map | ||||||||||||
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Annotation | Refinement half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Refinement half-map 2
File | emd_42815_half_map_2.map | ||||||||||||
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Annotation | Refinement half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PNMA2 icosahedral capsid
Entire | Name: PNMA2 icosahedral capsid |
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Components |
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-Supramolecule #1: PNMA2 icosahedral capsid
Supramolecule | Name: PNMA2 icosahedral capsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 2.49 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.4 / Details: phosphate buffered saline, pH 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 17600 / Average exposure time: 0.6 sec. / Average electron dose: 30.68 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |