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Yorodumi- EMDB-41485: Subtomogram averaged consensus structure of the malarial 80S ribo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41485 | ||||||||||||
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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 | ||||||||||||
Sample |
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Keywords | ribosome / malaria / cryoET / in situ / Plasmodium falciparum / translation | ||||||||||||
Function / homology | Function and homology information RMTs methylate histone arginines / Major pathway of rRNA processing in the nucleolus and cytosol / Protein methylation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / Metalloprotease DUBs ...RMTs methylate histone arginines / Major pathway of rRNA processing in the nucleolus and cytosol / Protein methylation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / 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 / Dual Incision 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 / Translation initiation complex formation / 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 / Negative regulators of DDX58/IFIH1 signaling / 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 / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / 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) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosome binding / kinase activity / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / ubiquitin-dependent protein catabolic process / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||||||||
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: To Be Published Title: Divergent translational landscape reflects adaptation to biased codon usage in malaria parasites Authors: Anton L / Cheng W / Haile M / Cobb DW / Zhu X / Han L / Li E / Nair A / Lee CL / Ho CM | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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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 | 90.6 KB 90.6 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 | 18.8 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 |
-Validation report
Summary document | emd_41485_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_41485_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_41485_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | emd_41485_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41485 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41485 | HTTPS FTP |
-Related structure data
Related structure data | 8tpuMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-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 |
-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 |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-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 |