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- PDB-5osg: Structure of KSRP in context of Leishmania donovani 80S -

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Basic information

Entry
Database: PDB / ID: 5osg
TitleStructure of KSRP in context of Leishmania donovani 80S
Components
  • 18S rRNA18S ribosomal RNA
  • 40S ribosomal protein S6
  • RNA binding protein, putative
KeywordsRIBOSOME / Kinetoplastids / cryo-EM / KSRP
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding
Similarity search - Function
Ribosomal protein S6, eukaryotic / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e signature. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Ribosomal protein S6, eukaryotic / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e signature. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / RNA binding protein, putative / Small ribosomal subunit protein eS6
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBrito Querido, J. / Mancera-Martinez, E. / Vicens, Q. / Bochler, A. / Chicher, J. / Simonetti, A. / Hashem, Y.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-14-ACHN-0024 France
LABEXANR-10-LABX-0036_NETRNA France
Citation
Journal: Structure / Year: 2017
Title: The cryo-EM Structure of a Novel 40S Kinetoplastid-Specific Ribosomal Protein.
Authors: Jailson Brito Querido / Eder Mancera-Martínez / Quentin Vicens / Anthony Bochler / Johana Chicher / Angelita Simonetti / Yaser Hashem /
Abstract: Kinetoplastids are potentially lethal protozoan pathogens affecting more than 20 million people worldwide. There is a critical need for more specific targets for the development of safer anti- ...Kinetoplastids are potentially lethal protozoan pathogens affecting more than 20 million people worldwide. There is a critical need for more specific targets for the development of safer anti-kinetoplastid therapeutic molecules that can replace the scarce and highly cytotoxic current drugs. The kinetoplastid ribosome represents a potential therapeutic target due to its relative structural divergence when compared with its human counterpart. However, several kinetoplastid-specific ribosomal features remain uncharacterized. Here, we present the near-atomic cryoelectron microscopy structure of a novel bona fide kinetoplastid-specific ribosomal (r-) protein (KSRP) bound to the ribosome. KSRP is an essential protein located at the solvent face of the 40S subunit, where it binds and stabilizes kinetoplastid-specific domains of rRNA, suggesting its role in ribosome integrity. KSRP also interacts with the r-protein eS6 at a region that is only conserved in kinetoplastids. The kinetoplastid-specific ribosomal environment of KSRP provides a promising target for the design of safer anti-kinetoplastidian drugs.
#1: 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
DepositionAug 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
h: RNA binding protein, putative
2: 18S rRNA
P: 40S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)763,8973
Polymers763,8973
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7240 Å2
ΔGint-49 kcal/mol
Surface area24670 Å2
MethodPISA

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Components

#1: Protein RNA binding protein, putative / KSRP


Mass: 25254.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: LDBPK_320790 / Production host: Leishmania donovani (eukaryote) / References: UniProt: E9BNI3
#2: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 710272.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Production host: Leishmania donovani (eukaryote) / References: GenBank: 9504
#3: Protein 40S ribosomal protein S6 / / eS6


Mass: 28370.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: RPS6, L3640.11, Lmj_1130, LmjF21.1780, LmjF_21_1780 / Production host: Leishmania donovani (eukaryote) / References: UniProt: Q9NE83

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 80S ribosomeEukaryotic ribosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Leishmania donovani (eukaryote)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213108 / Symmetry type: POINT

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