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- PDB-3j0q: Core of mammalian 80S pre-ribosome in complex with tRNAs fitted t... -

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Basic information

Entry
Database: PDB / ID: 3j0q
TitleCore of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 10.6A cryo-em map: rotated PRE state 2
Components
  • (40S ribosomal RNA ...) x 7
  • (60S ribosomal RNA ...) x 4
  • (Ribosomal protein ...) x 6
  • (mRNA fragment) x 2
  • tRNATransfer RNA
KeywordsRIBOSOME / Mammalia / translation / elongation cycle / tRNA
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / maturation of LSU-rRNA / ribosomal large subunit assembly / cytosolic large ribosomal subunit ...SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / maturation of LSU-rRNA / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / RNA binding / nucleus / cytosol
Similarity search - Function
Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L5, conserved site / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. ...Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L5, conserved site / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L5 / ribosomal L5P family C-terminus
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL5B
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.6 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 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: em_image_scans / em_software / struct_ref_seq
Item: _em_software.image_processing_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
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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  • Simplified surface model + fitted atomic model
  • EMDB-5329
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
a: 40S ribosomal RNA fragment
c: 40S ribosomal RNA fragment
d: 40S ribosomal RNA fragment
g: 40S ribosomal RNA fragment
G: 40S ribosomal RNA fragment
f: 40S ribosomal RNA fragment
h: 40S ribosomal RNA fragment
S: Ribosomal protein S15
L: Ribosomal protein S23
X: Ribosomal protein S30
2: 60S ribosomal RNA fragment
3: 60S ribosomal RNA fragment
9: 60S ribosomal RNA fragment
7: 60S ribosomal RNA fragment
B: Ribosomal protein L10a
J: Ribosomal protein L10
k: Ribosomal protein L11
Y: tRNA
y: mRNA fragment
W: tRNA
w: mRNA fragment


Theoretical massNumber of molelcules
Total (without water)298,46421
Polymers298,46421
Non-polymers00
Water0
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 ... , 7 types, 7 molecules acdgGfh

#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: 5426.301 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: 2283.459 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: 9934.950 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: 4132.518 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: 6794.028 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: 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 ... , 6 types, 6 molecules SLXBJk

#8: 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
#9: 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
#10: 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 L10a / Ribosome


Mass: 24014.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver / References: UniProt: P0CX43*PLUS
#16: 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
#17: Protein Ribosomal protein L11 /


Mass: 18780.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver / References: UniProt: Q3E757*PLUS

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60S ribosomal RNA ... , 4 types, 4 molecules 2397

#11: 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
#12: 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
#13: RNA chain 60S ribosomal RNA fragment


Mass: 6108.737 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#14: 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

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RNA chain , 3 types, 4 molecules YWyw

#18: RNA chain tRNA / Transfer RNA


Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#19: RNA chain mRNA fragment


Mass: 872.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: liver
#20: 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 DERIVED FROM PDB ENTRY 2XSY (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: Mammalian 80S-PRE complex in rotated 2 state / 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 / Details: LOW DOSE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / 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 / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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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: SINGLE PARTICLESingle particle analysis / Resolution: 10.6 Å / Num. of particles: 23347 / Nominal pixel size: 2.52 Å / Actual pixel size: 2.52 Å / Details: PROJECTION MATCHING / Symmetry type: POINT
Atomic model building
IDProtocolSpaceDetails
1RIGID BODY FITREALMETHOD--LOCAL RIGID BODY DOCKING REFINEMENT PROTOCOL--RIGID BODY DOCKING DETAILS--RIGID BODY DOCKING CARRIED OUT WITH THE CHIMERA SOFTWARE PACKAGE DETAILS--40S
2DETAILS--60S
Atomic model building

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

IDPDB-IDAccession codeDetailsInitial refinement model-ID
12XZM

2xzm
PDB Unreleased entry

2XZM40S1
23O58

3o58
PDB Unreleased entry

3O5860S2
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms5528 12799 0 0 18327

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