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Open data
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Basic information
Entry | Database: PDB / ID: 1ysh | ||||||
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Title | Localization and dynamic behavior of ribosomal protein L30e | ||||||
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![]() | STRUCTURAL PROTEIN/RNA / STRUCTURAL PROTEIN / RNA / STRUCTURAL PROTEIN-RNA COMPLEX | ||||||
Function / homology | ![]() small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / ribosome / structural constituent of ribosome / translation / nucleolus / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å | ||||||
![]() | Halic, M. / Becker, T. / Frank, J. / Spahn, C.M. / Beckmann, R. | ||||||
![]() | ![]() Title: Localization and dynamic behavior of ribosomal protein L30e. Authors: Mario Halic / Thomas Becker / Joachim Frank / Christian M T Spahn / Roland Beckmann / ![]() Abstract: The ribosomal protein L30e is an indispensable component of the eukaryotic 80S ribosome, where it is part of the large (60S) ribosomal subunit. Here, we determined the localization of L30e in the ...The ribosomal protein L30e is an indispensable component of the eukaryotic 80S ribosome, where it is part of the large (60S) ribosomal subunit. Here, we determined the localization of L30e in the cryo-EM map of the 80S wheat germ (wg) ribosome at a resolution of 9.5 A. L30e is part of the interface between large and small subunits, where it dynamically participates in the formation of the two intersubunit bridges eB9 and B4. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.9 KB | Display | ![]() |
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PDB format | ![]() | 106.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1125MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 3 types, 3 molecules AFB
#1: RNA chain | Mass: 9159.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 11055.686 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: RNA chain | Mass: 32985.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Ribosomal protein ... , 2 types, 2 molecules CD
#4: Protein | Mass: 11512.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#5: Protein | Mass: 8003.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 1 types, 1 molecules E
#6: Protein | Mass: 9914.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 80s wheat germ ribosome / Type: RIBOSOME |
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Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Cryogen name: ETHANE / Details: PLUNGED INTO ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 / Date: Jan 1, 2000 Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 38250 X / Calibrated magnification: 38300 X / Nominal defocus max: 45000 nm / Nominal defocus min: 7000 nm / Cs: 2 mm |
Specimen holder | Temperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 190 |
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Processing
Software | Name: SPIDER / Classification: refinement | ||||||||||||
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EM software | Name: SPIDER / Category: 3D reconstruction | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 21000 / Nominal pixel size: 2.04 Å / Actual pixel size: 2.04 Å / Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 9.5 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 9.5 Å
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