- EMDB-8343: Cryo-EM structure of the Leishmania donovani 80S ribosome at 2.9 ... -
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Basic information
Entry
Database: EMDB / ID: EMD-8343
Title
Cryo-EM structure of the Leishmania donovani 80S ribosome at 2.9 Angstrom resolution
Map data
Leishmania donovani 80S ribosome
Sample
Complex: 80S ribosome
Function / homology
Function and homology information
protein-RNA complex assembly / translation regulator activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding ...protein-RNA complex assembly / translation regulator activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / cytoplasm Similarity search - Function
Ribosomal protein L28e / : / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily ...Ribosomal protein L28e / : / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Plectin/S10, N-terminal / Plectin/S10 domain / : / Ribosomal protein L44e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L10e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein L44e / Ribosomal protein L44 / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / 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 / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S6, eukaryotic / Ribosomal protein L30e, conserved site / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein L27e / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein L30/YlxQ / 60S ribosomal protein L35 / Ribosomal protein L7A/L8 / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S8e / Ribosomal protein L18e / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein L37ae / Ribosomal L37ae protein family / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal_L19e / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein S6e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein L39e / Ribosomal protein L14e domain / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein Similarity search - Domain/homology
60S ribosomal protein L23a / Ribosomal protein L38, putative / 60S ribosomal protein L10, putative / 60S ribosomal protein L19, putative / 60S ribosomal protein L7a / Large ribosomal subunit protein eL28 / 40S ribosomal protein S15A, putative / 40S ribosomal protein S4 / 60S ribosomal protein L44, putative / 60S ribosomal protein L39, putative ...60S ribosomal protein L23a / Ribosomal protein L38, putative / 60S ribosomal protein L10, putative / 60S ribosomal protein L19, putative / 60S ribosomal protein L7a / Large ribosomal subunit protein eL28 / 40S ribosomal protein S15A, putative / 40S ribosomal protein S4 / 60S ribosomal protein L44, putative / 60S ribosomal protein L39, putative / 60S ribosomal protein L9, putative / 60S ribosomal protein L37a / 60S ribosomal protein L11 (L5, L16) / 60S ribosomal protein L17, putative / 40S ribosomal protein S8 / 60S ribosomal protein L7, putative / 40S ribosomal protein S16, putative / 60S ribosomal protein L35, putative / Ribosomal protein S10 / Ribosomal protein S29, putative / Ribosomal protein L1a, putative / 40S ribosomal protein S30 / Ribosomal protein L15 / Ubiquitin-60S ribosomal protein L40 / RNA binding protein, putative / Ribosomal L27e family protein / Ribosomal protein L35Ae family protein / 40S ribosomal protein S19 protein, putative / 60S ribosomal protein L21, putative / 60S ribosomal protein L30 / 40S ribosomal protein S3a / 60S ribosomal protein L18a / 60S ribosomal protein L5, putative / 60S Ribosomal protein L36, putative / 60S ribosomal protein L32 / 60S ribosomal subunit protein L31, putative / 60S ribosomal protein L27A/L29, putative / 60S ribosomal protein L23, putative / 40S ribosomal protein S18, putative / 40S ribosomal protein S10, putative / 40S ribosomal protein S9, putative / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL34 / 60S ribosomal protein L18, putative / Large ribosomal subunit protein eL37 / Probable 60S ribosomal protein L14 / 40S ribosomal protein S5 / Guanine nucleotide-binding protein subunit beta-like protein / Small ribosomal subunit protein eS6 Similarity search - Component
Biological species
Leishmania donovani (eukaryote)
Method
single particle reconstruction / cryo EM / Resolution: 2.9 Å
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM071940
United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)
DE025567
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
AI094386
United States
National Institutes of Health/Office of the Director
1S10OD018111
United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)
1S10RR23057
United States
National Science Foundation (NSF, United States)
DBI-338135
United States
Citation
Journal: Nat Commun / Year: 2016 Title: Structures and stabilization of kinetoplastid-specific split rRNAs revealed by comparing leishmanial and human ribosomes. Authors: Xing Zhang / Mason Lai / Winston Chang / Iris Yu / Ke Ding / Jan Mrazek / Hwee L Ng / Otto O Yang / Dmitri A Maslov / Z Hong Zhou / Abstract: The recent success in ribosome structure determination by cryoEM has opened the door to defining structural differences between ribosomes of pathogenic organisms and humans and to understand ribosome- ...The recent success in ribosome structure determination by cryoEM has opened the door to defining structural differences between ribosomes of pathogenic organisms and humans and to understand ribosome-targeting antibiotics. Here, by direct electron-counting cryoEM, we have determined the structures of the Leishmania donovani and human ribosomes at 2.9 Å and 3.6 Å, respectively. Our structure of the leishmanial ribosome elucidates the organization of the six fragments of its large subunit rRNA (as opposed to a single 28S rRNA in most eukaryotes, including humans) and reveals atomic details of a unique 20 amino acid extension of the uL13 protein that pins down the ends of three of the rRNA fragments. The structure also fashions many large rRNA expansion segments. Direct comparison of our human and leishmanial ribosome structures at the decoding A-site sheds light on how the bacterial ribosome-targeting drug paromomycin selectively inhibits the eukaryotic L. donovani, but not human, ribosome.
History
Deposition
Aug 19, 2016
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Header (metadata) release
Oct 26, 2016
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Map release
Oct 26, 2016
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Update
Dec 25, 2019
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Current status
Dec 25, 2019
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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