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Yorodumi- EMDB-41485: Subtomogram averaged consensus structure of the malarial 80S ribo... -
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Open data
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Basic information
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| Title | Subtomogram averaged consensus structure of the malarial 80S ribosome in Plasmodium falciparum-infected human erythrocytes | ||||||||||||
Map data | In situ consensus reconstruction of Plasmodium falciparum parasite Pf80S ribosome | ||||||||||||
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Keywords | ribosome / malaria / cryoET / in situ / Plasmodium falciparum / translation | ||||||||||||
| Function / homology | Function and homology informationRMTs methylate histone arginines / : / Protein methylation / Translesion synthesis by REV1 / : / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / Metalloprotease DUBs ...RMTs methylate histone arginines / : / Protein methylation / Translesion synthesis by REV1 / : / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / Metalloprotease DUBs / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / : / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / ER Quality Control Compartment (ERQC) / Iron uptake and transport / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / : / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / : / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / : / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Aggrephagy / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / MAPK6/MAPK4 signaling / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / maturation of LSU-rRNA / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / rescue of stalled cytosolic ribosome / protein kinase C binding / chloroplast / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / kinase activity / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
| Biological species | ![]() | ||||||||||||
| Method | subtomogram averaging / cryo EM / Resolution: 4.1 Å | ||||||||||||
Authors | Anton L / Cheng W / Zhu X / Ho CM | ||||||||||||
| Funding support | United States, Switzerland, France, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2025Title: Integrated structural biology of the native malarial translation machinery and its inhibition by an antimalarial drug. Authors: Leonie Anton / Wenjing Cheng / Meseret T Haile / Jerzy M Dziekan / David W Cobb / Xiyan Zhu / Leyan Han / Emerson Li / Anjali Nair / Carolyn L Lee / Hanyu Wang / Hangjun Ke / Guoan Zhang / ...Authors: Leonie Anton / Wenjing Cheng / Meseret T Haile / Jerzy M Dziekan / David W Cobb / Xiyan Zhu / Leyan Han / Emerson Li / Anjali Nair / Carolyn L Lee / Hanyu Wang / Hangjun Ke / Guoan Zhang / Emma H Doud / Alan F Cowman / Chi-Min Ho / ![]() Abstract: Our understanding of cellular events is hampered by the gap between the resolution at which we can observe events inside cells and our ability to replicate physiological conditions in test tubes. ...Our understanding of cellular events is hampered by the gap between the resolution at which we can observe events inside cells and our ability to replicate physiological conditions in test tubes. Here, we show in Plasmodium falciparum, a non-model organism of high medical importance, that this gap can be bridged by using an integrated structural biology approach to visualize events inside the cell at molecular resolution. We determined eight high-resolution structures of the native malarial ribosome in actively translating states inside P. falciparum-infected human erythrocytes using in situ cryo-electron tomography. Following perturbation with a Plasmodium-specific translation inhibitor, we then observed a decrease in elongation factor-bound ribosomal states and an apparent upregulation of ribosome biogenesis in inhibitor-treated parasites. Our work elucidates new molecular details of the malarial translation elongation cycle and demonstrates direct multiscale visualization of drug-induced phenotypic changes in the structure and localization of individual molecules within the native cellular context. | ||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_41485.map.gz | 77.6 MB | EMDB map data format | |
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| Header (meta data) | emd-41485-v30.xml emd-41485.xml | 94.5 KB 94.5 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_41485_fsc.xml | 10.5 KB | Display | FSC data file |
| Images | emd_41485.png | 73.4 KB | ||
| Filedesc metadata | emd-41485.cif.gz | 19.5 KB | ||
| Others | emd_41485_half_map_1.map.gz emd_41485_half_map_2.map.gz | 77.8 MB 77.7 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41485 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41485 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8tpuMC ![]() 9bupC ![]() 9buqC ![]() 9busC ![]() 9butC ![]() 9buuC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_41485.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | In situ consensus reconstruction of Plasmodium falciparum parasite Pf80S ribosome | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.69 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: Half map 1 of in situ consensus reconstruction...
| File | emd_41485_half_map_1.map | ||||||||||||
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| Annotation | Half map 1 of in situ consensus reconstruction of Plasmodium falciparum parasite Pf80S ribosome | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Half map 2 of in situ consensus reconstruction...
| File | emd_41485_half_map_2.map | ||||||||||||
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| Annotation | Half map 2 of in situ consensus reconstruction of Plasmodium falciparum parasite Pf80S ribosome | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : Plasmodium falciparum 80S ribosome consensus structure
+Supramolecule #1: Plasmodium falciparum 80S ribosome consensus structure
+Macromolecule #1: 40S ribosomal protein S24
+Macromolecule #2: 40S ribosomal protein S25
+Macromolecule #3: 40S ribosomal protein S26
+Macromolecule #4: 40S ribosomal protein S27
+Macromolecule #5: 60S ribosomal protein L41
+Macromolecule #6: Small ribosomal subunit protein eS30
+Macromolecule #9: 40S ribosomal protein S3a
+Macromolecule #10: 40S ribosomal protein SA
+Macromolecule #11: 40S ribosomal protein S3
+Macromolecule #12: 40S ribosomal protein S9, putative
+Macromolecule #13: 40S ribosomal protein S4
+Macromolecule #14: 40S ribosomal protein S5
+Macromolecule #15: 40S ribosomal protein S6
+Macromolecule #16: 40S ribosomal protein S5, putative
+Macromolecule #17: 40S ribosomal protein S7
+Macromolecule #18: 40S ribosomal protein S15A, putative
+Macromolecule #19: 40S ribosomal protein S8
+Macromolecule #20: 40S ribosomal protein S16
+Macromolecule #21: 40S ribosomal protein S20e, putative
+Macromolecule #22: 40S ribosomal protein S10, putative
+Macromolecule #23: 40S ribosomal protein S11
+Macromolecule #24: 40S ribosomal protein S23, putative
+Macromolecule #25: 40S ribosomal protein S12
+Macromolecule #26: 40S ribosomal protein S18, putative
+Macromolecule #27: 40S ribosomal protein S29, putative
+Macromolecule #28: 40S ribosomal protein S15
+Macromolecule #29: 40S ribosomal protein S11, putative
+Macromolecule #30: 40S ribosomal protein S17, putative
+Macromolecule #31: 40S ribosomal protein S19
+Macromolecule #32: 40S ribosomal protein S19
+Macromolecule #33: 40S ribosomal protein S21
+Macromolecule #37: 60S ribosomal protein L13
+Macromolecule #38: 60S ribosomal protein L27
+Macromolecule #39: 60S ribosomal protein L28
+Macromolecule #40: 60S ribosomal protein L29
+Macromolecule #41: 60S ribosomal protein L30e, putative
+Macromolecule #42: 60S ribosomal protein L31
+Macromolecule #43: 60S ribosomal protein L14, putative
+Macromolecule #44: 60S ribosomal protein L32
+Macromolecule #45: 60S ribosomal protein L35ae, putative
+Macromolecule #46: 60S ribosomal protein L34
+Macromolecule #47: 60S ribosomal protein L36
+Macromolecule #48: 60S ribosomal protein L38
+Macromolecule #49: 60S ribosomal protein L39
+Macromolecule #50: Ubiquitin-60S ribosomal protein L40
+Macromolecule #51: Ribosomal protein L15
+Macromolecule #52: Large ribosomal subunit protein eL43
+Macromolecule #53: Large ribosomal subunit protein eL42
+Macromolecule #54: 60S ribosomal protein L6, putative
+Macromolecule #55: 60S ribosomal protein L7a
+Macromolecule #56: Ribosomal protein L37
+Macromolecule #57: 60S ribosomal protein L13, putative
+Macromolecule #58: 60S ribosomal protein L23, putative
+Macromolecule #59: 60S ribosomal protein L18-2, putative
+Macromolecule #60: 60S ribosomal protein L27a, putative
+Macromolecule #61: 60S ribosomal protein L10, putative
+Macromolecule #62: 60S ribosomal protein L5, putative
+Macromolecule #63: 60S ribosomal protein L17, putative
+Macromolecule #64: 60S ribosomal protein L23
+Macromolecule #65: 60S ribosomal protein L19
+Macromolecule #66: 60S ribosomal protein L26, putative
+Macromolecule #67: 60S ribosomal protein L35, putative
+Macromolecule #68: 60S ribosomal protein L7, putative
+Macromolecule #69: 60S ribosomal protein L2
+Macromolecule #70: 60S ribosomal protein L3
+Macromolecule #71: 60S ribosomal protein L4
+Macromolecule #72: 60S ribosomal protein L11a, putative
+Macromolecule #73: 60S ribosomal protein L18a
+Macromolecule #74: 60S ribosomal protein L6, putative
+Macromolecule #75: 60S ribosomal protein L21
+Macromolecule #76: 60S ribosomal protein L41
+Macromolecule #77: 60S ribosomal protein L22, putative
+Macromolecule #78: 60S ribosomal protein L24, putative
+Macromolecule #79: Receptor for activated c kinase
+Macromolecule #7: 60S ribosomal protein L24, putative
+Macromolecule #8: 18S ribosomal RNA
+Macromolecule #34: 28S ribosomal RNA
+Macromolecule #35: 5.8S ribosomal RNA
+Macromolecule #36: 5S ribosomal RNA
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | subtomogram averaging |
| Aggregation state | cell |
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Sample preparation
| Buffer | pH: 7.2 |
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| Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.93 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 2.8000000000000003 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Authors
United States,
Switzerland,
France, 3 items
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Processing
FIELD EMISSION GUN

