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- EMDB-3280: Biochemical and structural characterization of the yeast Sdo1p su... -

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Entry
Database: EMDB / ID: EMD-3280
TitleBiochemical and structural characterization of the yeast Sdo1p suggests a surveillance role in the 60S ribosomal subunit maturation
Map dataReconstruction of 60S-Sdo1p complex.
Sample
  • Sample: The dimeric structure of the yeast 60S ribosomal subunits bound with Sdo1p
  • Complex: Sdo1p bound 60S subunit
  • Protein or peptide: Sdo1p
KeywordsRibosome biogenesis / SBDS / SDS / Sdo1 / cryo-electron microscopy (cryo-EM)
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsMa CY / Yan KG / Tan D / Li NN / Zhang YX / Yuan Y / Li ZF / Dong MQ / Lei JL / Gao N
CitationJournal: Protein Cell / Year: 2016
Title: Structural dynamics of the yeast Shwachman-Diamond syndrome protein (Sdo1) on the ribosome and its implication in the 60S subunit maturation.
Authors: Chengying Ma / Kaige Yan / Dan Tan / Ningning Li / Yixiao Zhang / Yi Yuan / Zhifei Li / Meng-Qiu Dong / Jianlin Lei / Ning Gao /
Abstract: The human Shwachman-Diamond syndrome (SDS) is an autosomal recessive disease caused by mutations in a highly conserved ribosome assembly factor SBDS. The functional role of SBDS is to cooperate with ...The human Shwachman-Diamond syndrome (SDS) is an autosomal recessive disease caused by mutations in a highly conserved ribosome assembly factor SBDS. The functional role of SBDS is to cooperate with another assembly factor, elongation factor 1-like (Efl1), to promote the release of eukaryotic initiation factor 6 (eIF6) from the late-stage cytoplasmic 60S precursors. In the present work, we characterized, both biochemically and structurally, the interaction between the 60S subunit and SBDS protein (Sdo1p) from yeast. Our data show that Sdo1p interacts tightly with the mature 60S subunit in vitro through its domain I and II, and is capable of bridging two 60S subunits to form a stable 2:2 dimer. Structural analysis indicates that Sdo1p bind to the ribosomal P-site, in the proximity of uL16 and uL5, and with direct contact to H69 and H38. The dynamic nature of Sdo1p on the 60S subunit, together with its strategic binding position, suggests a surveillance role of Sdo1p in monitoring the conformational maturation of the ribosomal P-site. Altogether, our data support a conformational signal-relay cascade during late-stage 60S maturation, involving uL16, Sdo1p, and Efl1p, which interrogates the functional P-site to control the departure of the anti-association factor eIF6.
History
DepositionDec 11, 2015-
Header (metadata) releaseJan 27, 2016-
Map releaseMar 30, 2016-
UpdateMar 30, 2016-
Current statusMar 30, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3280_60S...

emd_3280.png

Downloads & links

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Map

FileDownload / File: emd_3280.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of 60S-Sdo1p complex.
Voxel sizeX=Y=Z: 2.76 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.03258364 - 0.11587372
Average (Standard dev.)-0.00059538 (±0.01439751)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 496.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z496.800496.800496.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0330.116-0.001

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Supplemental data

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Sample components

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Entire : The dimeric structure of the yeast 60S ribosomal subunits bound w...

EntireName: The dimeric structure of the yeast 60S ribosomal subunits bound with Sdo1p
Components
  • Sample: The dimeric structure of the yeast 60S ribosomal subunits bound with Sdo1p
  • Complex: Sdo1p bound 60S subunit
  • Protein or peptide: Sdo1p

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Supramolecule #1000: The dimeric structure of the yeast 60S ribosomal subunits bound w...

SupramoleculeName: The dimeric structure of the yeast 60S ribosomal subunits bound with Sdo1p
type: sample / ID: 1000 / Oligomeric state: two Sdo1p binding to two 60S subunit / Number unique components: 2

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Supramolecule #1: Sdo1p bound 60S subunit

SupramoleculeName: Sdo1p bound 60S subunit / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: LSU 60S
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: yeast

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Macromolecule #1: Sdo1p

MacromoleculeName: Sdo1p / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: yeast

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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

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm
Sample stageSpecimen holder: Gatan CT3500 / Specimen holder model: OTHER
DateDec 8, 2011
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k)
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: ctfindIII
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: OTHER / Software - Name: Spider, relion / Number images used: 13219
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3o58
PDB Unreleased entry

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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