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- EMDB-3886: Cryo-EM structure of a late pre-40S ribosomal subunit from Saccha... -

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Entry
Database: EMDB / ID: 3886
TitleCryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae
Map dataCryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae
Samplepre-40S ribosomal subunit from Saccharomyces cerevisiae:
Function / homologyRibosomal protein S19e domain superfamily / Ribosomal protein S21e / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / KOW motif / Ribosomal S17 / Ribosomal family S4e / Ribosomal S3Ae family / Ribosomal protein S19e ...Ribosomal protein S19e domain superfamily / Ribosomal protein S21e / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / KOW motif / Ribosomal S17 / Ribosomal family S4e / Ribosomal S3Ae family / Ribosomal protein S19e / Ribosomal protein S6e / Ribosomal protein S28e / Ribosomal protein S8e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S7e / Ribosomal protein S17 / Ribosomal protein S24e / S4 domain / Ribosomal protein S27a / Ribosomal protein S27 / S25 ribosomal protein / Ribosomal protein S5, C-terminal domain / Ribosomal protein S30 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / Bystin / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / AARP2CN (NUC121) domain / Rio2, N-terminal / Ribosomal protein S9/S16 / Ribosomal protein S5, N-terminal domain / Ribosomal_S17 N-terminal / Ribosomal protein S8 superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S7 domain / 30s ribosomal protein S13, C-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Bms1/Tsr1-type G domain / Serine/threonine-protein kinase Rio2 / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S15 / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / K Homology domain, type 1 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S21e superfamily / S27a-like superfamily / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S19 / Ubiquitin family / 40S ribosomal protein S4 C-terminus / Ribosomal protein S7 signature. / Formation of a pool of free 40S subunits / UCH proteinases / mTORC1-mediated signalling / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / SCF(Skp2)-mediated degradation of p27/p21 / RMTs methylate histone arginines / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / Negative regulation of MAPK pathway / MAPK6/MAPK4 signaling / Ub-specific processing proteases / Translesion Synthesis by POLH / Metalloprotease DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / rt:r-sce-69229: / L13a-mediated translational silencing of Ceruloplasmin expression / Recognition of DNA damage by PCNA-containing replication complex / Ribosomal protein S8 signature. / Ribosomal protein S4 signature. / Ribosomal protein S11 signature. / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ubiquitin domain signature. / Ribosomal protein S19 signature.
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsHeuer A / Thomson E / Schmidt C / Berninghausen O / Becker T / Hurt E / Beckmann R
CitationJournal: Elife / Year: 2017
Title: Cryo-EM structure of a late pre-40S ribosomal subunit from .
Authors: André Heuer / Emma Thomson / Christian Schmidt / Otto Berninghausen / Thomas Becker / Ed Hurt / Roland Beckmann
Validation ReportPDB-ID: 6eml

SummaryFull reportAbout validation report
DateDeposition: Sep 28, 2017 / Header (metadata) release: Oct 12, 2016 / Map release: Nov 29, 2017 / Last update: Mar 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0722
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0722
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6eml
  • Surface level: 0.0722
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3886.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.08 Å/pix.
= 416.256 Å
384 pix
1.08 Å/pix.
= 416.256 Å
384 pix
1.08 Å/pix.
= 416.256 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour Level:0.0722 (by author), 0.0722 (movie #1):
Minimum - Maximum-0.2616892 - 0.5234815
Average (Standard dev.)0.00002545438 (0.016299982)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 416.25598 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z416.256416.256416.256
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.2620.5230.000

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Supplemental data

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Sample components

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Entire pre-40S ribosomal subunit from Saccharomyces cerevisiae

EntireName: pre-40S ribosomal subunit from Saccharomyces cerevisiae
Number of components: 1
MassTheoretical: 1.2 MDa

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Component #1: protein, pre-40S ribosomal subunit from Saccharomyces cerevisiae

ProteinName: pre-40S ribosomal subunit from Saccharomyces cerevisiae
Recombinant expression: No
MassTheoretical: 1.2 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 1 %

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.4 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: - 2400.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 84100
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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