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Yorodumi- EMDB-26671: Rhoptry secretory apparatus of Plasmodium falciparum with an asso... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26671 | |||||||||
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Title | Rhoptry secretory apparatus of Plasmodium falciparum with an associated rhoptry tip from a non-fused rhoptry pair | |||||||||
Map data | Rhoptry secretory apparatus of Plasmodium falciparum with an associated rhoptry tip from a non-fused rhoptry pair | |||||||||
Sample |
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Keywords | Exocytosis Membrane Parasite / CELL INVASION | |||||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 50.0 Å | |||||||||
Authors | Martinez M / Chang Y-W | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Microbiol / Year: 2022 Title: Rhoptry secretion system structure and priming in Plasmodium falciparum revealed using in situ cryo-electron tomography. Authors: Matthew Martinez / William David Chen / Marta Mendonça Cova / Petra Molnár / Shrawan Kumar Mageswaran / Amandine Guérin / Audrey R Odom John / Maryse Lebrun / Yi-Wei Chang / Abstract: Apicomplexan parasites secrete contents of the rhoptries, club-shaped organelles in the apical region, into host cells to permit their invasion and establishment of infection. The rhoptry secretory ...Apicomplexan parasites secrete contents of the rhoptries, club-shaped organelles in the apical region, into host cells to permit their invasion and establishment of infection. The rhoptry secretory apparatus (RSA), which is critical for rhoptry secretion, was recently discovered in Toxoplasma and Cryptosporidium. It is unknown whether a similar molecular machinery exists in the malaria parasite Plasmodium. In this study, we use in situ cryo-electron tomography to investigate the rhoptry secretion system in P. falciparum merozoites. We identify the presence of an RSA at the cell apex and a morphologically distinct apical vesicle docking the tips of the two rhoptries to the RSA. We also discover two additional rhoptry organizations that lack the apical vesicle. Using subtomogram averaging, we reveal different conformations of the RSA structure corresponding to different rhoptry organizations. Our results highlight previously unknown steps in the process of rhoptry secretion and indicate a regulatory role for the conserved apical vesicle in host invasion by apicomplexan parasites. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26671.map.gz | 2.5 MB | EMDB map data format | |
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Header (meta data) | emd-26671-v30.xml emd-26671.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26671_fsc.xml | 3.3 KB | Display | FSC data file |
Images | emd_26671.png | 62.1 KB | ||
Masks | emd_26671_msk_1.map | 2.8 MB | Mask map | |
Filedesc metadata | emd-26671.cif.gz | 5 KB | ||
Others | emd_26671_half_map_1.map.gz emd_26671_half_map_2.map.gz | 1.3 MB 1.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26671 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26671 | HTTPS FTP |
-Validation report
Summary document | emd_26671_validation.pdf.gz | 810.7 KB | Display | EMDB validaton report |
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Full document | emd_26671_full_validation.pdf.gz | 810.2 KB | Display | |
Data in XML | emd_26671_validation.xml.gz | 9 KB | Display | |
Data in CIF | emd_26671_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26671 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26671 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26671.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Rhoptry secretory apparatus of Plasmodium falciparum with an associated rhoptry tip from a non-fused rhoptry pair | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 10.6 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26671_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Rhoptry secretory apparatus of Plasmodium falciparum with an...
File | emd_26671_half_map_1.map | ||||||||||||
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Annotation | Rhoptry secretory apparatus of Plasmodium falciparum with an associated rhoptry tip from a non-fused rhoptry pair | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Rhoptry secretory apparatus of Plasmodium falciparum with an...
File | emd_26671_half_map_2.map | ||||||||||||
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Annotation | Rhoptry secretory apparatus of Plasmodium falciparum with an associated rhoptry tip from a non-fused rhoptry pair | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Plasmodium falciparum merozoite
Entire | Name: Plasmodium falciparum merozoite |
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Components |
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-Supramolecule #1: Plasmodium falciparum merozoite
Supramolecule | Name: Plasmodium falciparum merozoite / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) |
-Supramolecule #2: Rhoptry secretory apparatus
Supramolecule | Name: Rhoptry secretory apparatus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 Details: 8-fold symmetric protein structure, anchored into the plasma membrane, which docks a rhoptry tip to the to the site of exocytosis at the plasma membrane |
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Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) / Organelle: Apical complex / Location in cell: Cytoplasm |
-Supramolecule #3: Rhoptry tip
Supramolecule | Name: Rhoptry tip / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2 Details: One of two rhoptry tips that is docked at the rhoptry secretory apparatus. |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 Details: RPMI medium modified with 27 mM NaHCO3, 11 mM glucose, 5 mM HEPES, 0.01 mM thymidine, 1 mM sodium pyruvate, 0.37 mM hypoxanthine, 10 ug/mL gentamicin, and 5 g/L Albumax |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 297 K / Instrument: LEICA EM GP Details: Blot for 4 or 6 seconds from the front before plunging. |
Details | Mechanically isolated merozoites from a highly synchronous culture of Plasmodium falciparum schizonts |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 9 / Average exposure time: 0.45 sec. / Average electron dose: 2.5 e/Å2 Details: Images were collected in dose-fractionation mode with 0.1 second exposure per frame, for a total of 0.4 or 0.5 seconds per tilt image |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 33000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |