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- 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
TitleCryo-EM structure of the Leishmania donovani 80S ribosome at 2.9 Angstrom resolution
Map dataLeishmania donovani 80S ribosome
Sample
  • Complex: 80S ribosome
Function / homology
Function and homology information


protein-RNA complex assembly / translation regulator activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit biogenesis / large ribosomal subunit / 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 from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit biogenesis / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / nucleolus / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Ribosomal protein L28e / Ribosomal protein L23 / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e ...: / Ribosomal protein L28e / Ribosomal protein L23 / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L10e, conserved site / Plectin/S10 domain / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L19, eukaryotic / Ribosomal protein S8e subdomain, eukaryotes / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L40e superfamily / 40S ribosomal protein S4 C-terminus / Ribosomal protein L30e signature 2. / Ribosomal protein S8e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S8e signature. / Ribosomal protein L30e, conserved site / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S6, eukaryotic / Ribosomal protein L14e domain / 60S ribosomal protein L19 / Ribosomal protein L14 / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / Ribosomal protein L30/YlxQ / RS4NT (NUC023) domain / Ribosomal protein L7A/L8 / 60S ribosomal protein L35 / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein L14 / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein L14, KOW motif / 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 L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein S8e / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein S3Ae
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-ribosomal protein eL40 fusion protein / 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 / Small ribosomal subunit protein eS1 / 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 / Large ribosomal subunit protein eL14 / 40S ribosomal protein S5 / LACK protective antigen / Small ribosomal subunit protein eS6
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang X / Lai M / Zhou ZH
Funding support United States, 6 items
OrganizationGrant numberCountry
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 Director1S10OD018111 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
CitationJournal: 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 19, 2016-
Header (metadata) releaseOct 26, 2016-
Map releaseOct 26, 2016-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
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  • Surface view colored by height
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-5t2a
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-5osg
  • Surface level: 0.006
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5osg
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8343.png

Downloads & links

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Map

FileDownload / File: emd_8343.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLeishmania donovani 80S ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 400 pix.
= 317.32 Å		0.79 Å/pix.
x 400 pix.
= 317.32 Å		0.79 Å/pix.
x 400 pix.
= 317.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7933 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.020437755 - 0.039144985
Average (Standard dev.)0.00007679666 (±0.0028778987)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 317.31998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.79330.79330.7933
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z317.320317.320317.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-0.0200.0390.000

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Supplemental data

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Sample components

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Entire : 80S ribosome

EntireName: 80S ribosome
Components
  • Complex: 80S ribosome

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Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Leishmania donovani (eukaryote) / Strain: 1S

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: EMDB MAP
EMDB ID:

2275

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 213108
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: OTHER

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