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- PDB-1ysh: Localization and dynamic behavior of ribosomal protein L30e -

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Basic information

Entry
Database: PDB / ID: 1ysh
TitleLocalization and dynamic behavior of ribosomal protein L30e
Components
  • (ribosomal protein ...) x 2
  • 40S RIBOSOMAL PROTEIN S13
  • RNA (101-MER)
  • RNA (28-MER)
  • RNA (34-MER)
KeywordsSTRUCTURAL PROTEIN/RNA / STRUCTURAL PROTEIN / RNA / STRUCTURAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


plastid / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / nucleolus / RNA binding / metal ion binding
Similarity search - Function
Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain ...Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L37ae/L37e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Zinc-binding ribosomal protein
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / Large ribosomal subunit protein eL43z / Large ribosomal subunit protein eL30 / 60S ribosomal protein L37a-1 / Small ribosomal subunit protein uS15z
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
Oryza sativa (Asian cultivated rice)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsHalic, M. / Becker, T. / Frank, J. / Spahn, C.M. / Beckmann, R.
CitationJournal: Nat Struct Mol Biol / Year: 2005
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.
History
DepositionFeb 8, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 18, 2019Group: Data collection / Database references / Source and taxonomy
Category: database_2 / em_software / pdbx_entity_src_syn / Item: _em_software.image_processing_id
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: RNA (28-MER)
F: RNA (34-MER)
B: RNA (101-MER)
C: ribosomal protein L30
D: ribosomal protein L37a
E: 40S RIBOSOMAL PROTEIN S13


Theoretical massNumber of molelcules
Total (without water)82,6326
Polymers82,6326
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules AFB

#1: RNA chain RNA (28-MER)


Mass: 9159.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (34-MER)


Mass: 11055.686 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (101-MER)


Mass: 32985.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Ribosomal protein ... , 2 types, 2 molecules CD

#4: Protein ribosomal protein L30


Mass: 11512.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K9
#5: Protein ribosomal protein L37a


Mass: 8003.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryza sativa (Asian cultivated rice) / References: UniProt: Q5QM99, UniProt: P0DKK1*PLUS

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Protein , 1 types, 1 molecules E

#6: Protein 40S RIBOSOMAL PROTEIN S13


Mass: 9914.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryza sativa (Asian cultivated rice) / References: GenBank: 50940531, UniProt: Q69UI2*PLUS

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Details

Has protein modificationY

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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 wheat germ ribosome / Type: RIBOSOME
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: PLUNGED INTO ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Jan 1, 2000
Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38250 X / Calibrated magnification: 38300 X / Nominal defocus max: 45000 nm / Nominal defocus min: 7000 nm / Cs: 2 mm
Specimen holderTemperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 190

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Processing

SoftwareName: SPIDER / Classification: refinement
EM softwareName: SPIDER / Category: 3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 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
RefinementHighest resolution: 9.5 Å
Refinement stepCycle: LAST / Highest resolution: 9.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 3517 0 0 5576

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