- EMDB-6456: Cryo-electron microscopy reconstruction of the P. falciparum 80S ... -
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Basic information
Entry
Database: EMDB / ID: EMD-6456
Title
Cryo-electron microscopy reconstruction of the P. falciparum 80S ribosome bound to P-tRNA
Map data
Cryo-EM reconstruction of the P. falciparum schizont-stage ribosome in a non-rotated state bound to P-tRNA
Sample
Sample: The schizont-stage Plasmodium falciparum 80S ribosome bound to P-tRNA
Complex: 80S ribosomeEukaryotic ribosome
Keywords
Cryo-EM / malaria / translational pausing / RACK1
Function / homology
Function and homology information
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 ...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 / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / 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) / Aggrephagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / : / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / 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 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) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / ribosomal large subunit assembly / mRNA 5'-UTR binding / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function
Ribosomal protein L41 / Ribosomal protein L41 / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / Ribosomal protein S26e / Ribosomal protein L29e ...Ribosomal protein L41 / Ribosomal protein L41 / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal protein S26e signature. / Ribosomal protein S2, eukaryotic / Ribosomal L29e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / : / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S12e signature. / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S12e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S4e, N-terminal, conserved site / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S19e signature. / Ribosomal protein S19e / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal protein L23/L25, N-terminal / Ribosomal L22e protein family / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein L30e, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein S23, eukaryotic/archaeal / 40S Ribosomal protein S10 / Ribosomal protein L23, N-terminal domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L30/YlxQ / Ribosomal protein S25 / S25 ribosomal protein / RS4NT (NUC023) domain / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L14e domain / 60S ribosomal protein L6E / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L34Ae / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L44e signature. / Ribosomal family S4e / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L32e, conserved site / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L19, eukaryotic / Ribosomal protein L7A/L8 / Ribosomal protein L34e / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L6e / Ribosomal protein L14 / Ribosomal protein L30, N-terminal / Ribosomal protein L14, KOW motif / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal L30 N-terminal domain / Ribosomal protein S4e signature. / Ribosomal protein L14 / Ribosomal protein S19A/S15e / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A Similarity search - Domain/homology
Ribosomal protein L15 / 60S ribosomal protein L39 / 40S ribosomal protein S29, putative / Ribosomal protein L37 / 40S ribosomal protein S19 / 60S ribosomal protein L18-2, putative / 60S ribosomal protein L19 / 60S ribosomal protein L27a, putative / 60S ribosomal protein L41 / 60S ribosomal protein L29 ...Ribosomal protein L15 / 60S ribosomal protein L39 / 40S ribosomal protein S29, putative / Ribosomal protein L37 / 40S ribosomal protein S19 / 60S ribosomal protein L18-2, putative / 60S ribosomal protein L19 / 60S ribosomal protein L27a, putative / 60S ribosomal protein L41 / 60S ribosomal protein L29 / 60S ribosomal protein L26, putative / 40S ribosomal protein S11, putative / 40S ribosomal protein S15A, putative / Large ribosomal subunit protein eL43 / 40S ribosomal protein S26 / Small ribosomal subunit protein eS30 / Large ribosomal subunit protein eL42 / 40S ribosomal protein S23, putative / Small ribosomal subunit protein eS12 / 60S ribosomal protein L7, putative / Small ribosomal subunit protein eS1 / 60S ribosomal protein L32 / 40S ribosomal protein S9, putative / 40S ribosomal protein S24 / 60S ribosomal protein L2 / 40S ribosomal protein S11 / 60S ribosomal protein L4 / 60S ribosomal protein L31 / 40S ribosomal protein S17, putative / 60S ribosomal protein L36 / 40S ribosomal protein S16, putative / 60S ribosomal protein L13 / Large ribosomal subunit protein eL22 / 40S ribosomal protein S5, putative / 40S ribosomal protein S10, putative / 60S ribosomal protein L11a, putative / 60S ribosomal protein L34 / Ubiquitin-60S ribosomal protein L40 / 40S ribosomal protein S15 / 60S ribosomal protein L17, putative / 40S ribosomal protein S6 / 60S ribosomal protein L18a / 60S ribosomal protein L6-2, putative / 60S ribosomal protein L23, putative / 60S ribosomal protein L23 / 60S ribosomal protein L6, putative / 60S ribosomal protein L24, putative / 40S ribosomal protein S27 / 40S ribosomal protein S7 / 40S ribosomal protein S19 / 40S ribosomal protein S21 / 60S ribosomal protein L35ae, putative / 60S ribosomal protein L28 / 60S ribosomal protein L38 / 40S ribosomal protein S18, putative / 60S ribosomal protein L35, putative / 40S ribosomal protein S4 / 60S ribosomal protein L3 / Small ribosomal subunit protein uS2 / 60S ribosomal protein L30e, putative / 60S ribosomal protein L13, putative / 40S ribosomal protein S20e, putative / 40S ribosomal protein S3 / 40S ribosomal protein S28e, putative / 60S ribosomal protein L27 / 40S ribosomal protein S5 / 60S ribosomal protein L14, putative / 60S ribosomal protein L21 / 60S ribosomal protein L7a / 60S ribosomal protein L5, putative / 40S ribosomal protein S25 / 60S ribosomal protein L10, putative / 40S ribosomal protein S8 Similarity search - Component
Biological species
Plasmodium falciparum (malaria parasite P. falciparum)
Method
single particle reconstruction / cryo EM / Resolution: 6.7 Å
Journal: Elife / Year: 2014 Title: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine. Authors: Wilson Wong / Xiao-chen Bai / Alan Brown / Israel S Fernandez / Eric Hanssen / Melanie Condron / Yan Hong Tan / Jake Baum / Sjors H W Scheres / Abstract: Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as ...Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as potential anti-malarial therapies. Antibiotics that inhibit protein translation are promising candidates for repositioning. We have solved the cryo-EM structure of the cytoplasmic ribosome from the human malaria parasite, Plasmodium falciparum, in complex with emetine at 3.2 Å resolution. Emetine is an anti-protozoan drug used in the treatment of ameobiasis that also displays potent anti-malarial activity. Emetine interacts with the E-site of the ribosomal small subunit and shares a similar binding site with the antibiotic pactamycin, thereby delivering its therapeutic effect by blocking mRNA/tRNA translocation. As the first cryo-EM structure that visualizes an antibiotic bound to any ribosome at atomic resolution, this establishes cryo-EM as a powerful tool for screening and guiding the design of drugs that target parasite translation machinery.
History
Deposition
Sep 4, 2015
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Header (metadata) release
Oct 14, 2015
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Map release
Oct 14, 2015
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Update
Dec 16, 2015
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Current status
Dec 16, 2015
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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