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- PDB-3j0l: Core of mammalian 80S pre-ribosome in complex with tRNAs fitted t... -

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Basic information

Entry
Database: PDB / ID: 3j0l
TitleCore of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 9.8A cryo-EM map: classic PRE state 1
Components
  • (40S ribosomal RNA ...) x 10
  • (60S ribosomal RNA ...) x 8
  • (Ribosomal protein ...) x 8
  • (mRNA fragment) x 2
  • tRNA
KeywordsRIBOSOME / Mammalia / translation / elongation cycle / tRNA
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.8 Å
AuthorsBudkevich, T. / Giesebrecht, J. / Altman, R. / Munro, J. / Mielke, T. / Nierhaus, K. / Blanchard, S. / Spahn, C.M.
CitationJournal: Mol Cell / Year: 2011
Title: Structure and dynamics of the mammalian ribosomal pretranslocation complex.
Authors: Tatyana Budkevich / Jan Giesebrecht / Roger B Altman / James B Munro / Thorsten Mielke / Knud H Nierhaus / Scott C Blanchard / Christian M T Spahn /
Abstract: Although the structural core of the ribosome is conserved in all kingdoms of life, eukaryotic ribosomes are significantly larger and more complex than their bacterial counterparts. The extent to ...Although the structural core of the ribosome is conserved in all kingdoms of life, eukaryotic ribosomes are significantly larger and more complex than their bacterial counterparts. The extent to which these differences influence the molecular mechanism of translation remains elusive. Multiparticle cryo-electron microscopy and single-molecule FRET investigations of the mammalian pretranslocation complex reveal spontaneous, large-scale conformational changes, including an intersubunit rotation of the ribosomal subunits. Through structurally related processes, tRNA substrates oscillate between classical and at least two distinct hybrid configurations facilitated by localized changes in their L-shaped fold. Hybrid states are favored within the mammalian complex. However, classical tRNA positions can be restored by tRNA binding to the E site or by the eukaryotic-specific antibiotic and translocation inhibitor cycloheximide. These findings reveal critical distinctions in the structural and energetic features of bacterial and mammalian ribosomes, providing a mechanistic basis for divergent translation regulation strategies and species-specific antibiotic action.
History
DepositionOct 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
a: 40S ribosomal RNA fragment
b: 40S ribosomal RNA fragment
c: 40S ribosomal RNA fragment
d: 40S ribosomal RNA fragment
e: 40S ribosomal RNA fragment
E: 40S ribosomal RNA fragment
f: 40S ribosomal RNA fragment
g: 40S ribosomal RNA fragment
G: 40S ribosomal RNA fragment
h: 40S ribosomal RNA fragment
T: Ribosomal protein S5
K: Ribosomal protein S14
L: Ribosomal protein S23
X: Ribosomal protein S30
S: Ribosomal protein S15
1: 60S ribosomal RNA fragment
2: 60S ribosomal RNA fragment
3: 60S ribosomal RNA fragment
4: 60S ribosomal RNA fragment
5: 60S ribosomal RNA fragment
6: 60S ribosomal RNA fragment
7: 60S ribosomal RNA fragment
8: 60S ribosomal RNA fragment
B: Ribosomal protein L10a
J: Ribosomal protein L10
F: Ribosomal protein L36a
Y: tRNA
y: mRNA fragment
V: tRNA
v: mRNA fragment
W: tRNA
w: mRNA fragment


Theoretical massNumber of molelcules
Total (without water)387,89132
Polymers387,89132
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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40S ribosomal RNA ... , 10 types, 10 molecules abcdeEfgGh

#1: RNA chain 40S ribosomal RNA fragment


Mass: 15500.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#2: RNA chain 40S ribosomal RNA fragment


Mass: 3876.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#3: RNA chain 40S ribosomal RNA fragment


Mass: 5426.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#4: RNA chain 40S ribosomal RNA fragment


Mass: 2283.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#5: RNA chain 40S ribosomal RNA fragment


Mass: 1223.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#6: RNA chain 40S ribosomal RNA fragment


Mass: 1482.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#7: RNA chain 40S ribosomal RNA fragment


Mass: 6794.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#8: RNA chain 40S ribosomal RNA fragment


Mass: 9934.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#9: RNA chain 40S ribosomal RNA fragment


Mass: 4132.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#10: RNA chain 40S ribosomal RNA fragment


Mass: 35735.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver

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Ribosomal protein ... , 8 types, 8 molecules TKLXSBJF

#11: Protein Ribosomal protein S5


Mass: 21662.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#12: Protein Ribosomal protein S14


Mass: 15218.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#13: Protein Ribosomal protein S23


Mass: 15646.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#14: Protein Ribosomal protein S30


Mass: 7893.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#15: Protein Ribosomal protein S15


Mass: 14027.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#24: Protein Ribosomal protein L10a


Mass: 24014.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#25: Protein Ribosomal protein L10


Mass: 25208.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#26: Protein Ribosomal protein L36a


Mass: 10955.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver

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60S ribosomal RNA ... , 8 types, 8 molecules 12345678

#16: RNA chain 60S ribosomal RNA fragment


Mass: 16044.528 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#17: RNA chain 60S ribosomal RNA fragment


Mass: 36097.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#18: RNA chain 60S ribosomal RNA fragment


Mass: 3859.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#19: RNA chain 60S ribosomal RNA fragment


Mass: 4572.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#20: RNA chain 60S ribosomal RNA fragment


Mass: 1875.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#21: RNA chain 60S ribosomal RNA fragment


Mass: 6218.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#22: RNA chain 60S ribosomal RNA fragment


Mass: 15929.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#23: RNA chain 60S ribosomal RNA fragment


Mass: 6462.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver

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RNA chain , 3 types, 6 molecules YVWyvw

#27: RNA chain tRNA


Mass: 24485.539 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#28: RNA chain mRNA fragment


Mass: 872.556 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#29: RNA chain mRNA fragment


Mass: 613.454 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver

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Details

Sequence detailsENTRY HAS BEEN MODELED WITH 60S RIBOSOMAL RNA AND PROTEINS FROM SACCHAROMYCES CEREVISIAE, 40S ...ENTRY HAS BEEN MODELED WITH 60S RIBOSOMAL RNA AND PROTEINS FROM SACCHAROMYCES CEREVISIAE, 40S RIBOSOMAL RNA AND PROTEINS FROM TETRAHYMENA THERMOPHILA, AND TRNA FROM THERMUS THERMOPHILUS.

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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: CORE OF MAMMALIAN 80S PRE-RIBOSOME IN COMPLEX WITH TRNAS
Type: RIBOSOME
Buffer solutionName: polyamine buffer / pH: 7.5 / Details: polyamine buffer
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Carbon coated Quantifoil grids
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: Ethane / Vitrobot (FEI) flash-frozen in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Oct 17, 2006
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 65520 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 77 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: CTF CORRECTION OF EACH DEFOCUS GROUP VOLUME PRIOR TO BACK PROJECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING / SPIDER / Resolution: 9.8 Å / Num. of particles: 30448 / Nominal pixel size: 2.52 Å / Actual pixel size: 2.52 Å / Symmetry type: POINT
Atomic model building
IDProtocolSpaceDetails
1RIGID BODY FITREALMETHOD--rigid body REFINEMENT PROTOCOL--rigid body DETAILS--40S
2DETAILS--60S
3DETAILS--tRNA
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeDetailsInitial refinement model-ID
12WDK

2wdk
PDB Unreleased entry

2WDKtRNA1
22XZM

2xzm
PDB Unreleased entry

2XZM40S2
33O58

3o58
PDB Unreleased entry

3O5860S3
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms7768 16773 0 0 24541

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