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- PDB-1mvr: Decoding Center & Peptidyl transferase center from the X-ray stru... -

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Basic information

Entry
Database: PDB / ID: 1mvr
TitleDecoding Center & Peptidyl transferase center from the X-ray structure of the Thermus thermophilus 70S ribosome, aligned to the low resolution Cryo-EM map of E.coli 70S Ribosome
Components
  • 30S RIBOSOMAL PROTEIN S12
  • 50S ribosomal protein L11
  • Helix 34 of 16S rRNA
  • Helix 44 of 16S rRNA
  • Helix 69 of 23S rRNA
  • Helix 89 of 23S rRNA
  • Helix 93 of 23S rRNA
  • mRNA, triplet codon (A-site)Messenger RNA
KeywordsRIBOSOME / RF2 / Release Complex / Conformational Changes
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain ...Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal protein S12, bacterial-type / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S12 signature. / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS12
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.8 Å
AuthorsRawat, U.B. / Zavialov, A.V. / Sengupta, J. / Valle, M. / Grassucci, R.A. / Linde, J. / Vestergaard, B. / Ehrenberg, M. / Frank, J.
Citation
Journal: Nature / Year: 2003
Title: A cryo-electron microscopic study of ribosome-bound termination factor RF2.
Authors: Urmila B S Rawat / Andrey V Zavialov / Jayati Sengupta / Mikel Valle / Robert A Grassucci / Jamie Linde / Bente Vestergaard / Måns Ehrenberg / Joachim Frank /
Abstract: Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into ...Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). RFs have a conserved GGQ amino-acid motif, which is crucial for peptide release and is believed to interact directly with the peptidyl-transferase centre (PTC) of the 50S ribosomal subunit. Another conserved motif of RFs (SPF in RF2) has been proposed to interact directly with stop codons in the DC of the 30S subunit. The distance between the DC and PTC is approximately 73 A. However, in the X-ray structure of RF2, SPF and GGQ are only 23 A apart, indicating that they cannot be at DC and PTC simultaneously. Here we show that RF2 is in an open conformation when bound to the ribosome, allowing GGQ to reach the PTC while still allowing SPF-stop-codon interaction. The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC.
#1: Journal: Science / Year: 2001
Title: Crystal structure of the ribosome at 5.5 A resolution
Authors: Yusupov, M.M. / Yusupova, G.Z. / Baucom, A. / Lieberman, K. / Earnest, T.N. / Cate, J.H. / Noller, H.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: The path of messenger RNA through the ribosome
Authors: Yusupova, G.Z. / Yusupov, M.M. / Cate, J.H. / Noller, H.
History
DepositionSep 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 14, 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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  • EMDB-1006
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  • EMDB-1007
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Structure viewerMolecule:
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Assembly

Deposited unit
1: mRNA, triplet codon (A-site)
A: Helix 34 of 16S rRNA
B: Helix 44 of 16S rRNA
C: Helix 69 of 23S rRNA
D: Helix 89 of 23S rRNA
E: Helix 93 of 23S rRNA
O: 30S RIBOSOMAL PROTEIN S12
L: 50S ribosomal protein L11


Theoretical massNumber of molelcules
Total (without water)110,2298
Polymers110,2298
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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RNA chain , 6 types, 6 molecules 1ABCDE

#1: RNA chain mRNA, triplet codon (A-site) / Messenger RNA / Coordinate model: P atoms only


Mass: 873.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: based on coordinates from 1GIX, 30S Subunit / Source: (natural) Escherichia coli (E. coli) / Strain: K12
#2: RNA chain Helix 34 of 16S rRNA / Coordinate model: P atoms only


Mass: 14465.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: based on coordinates from 1GIX, 30S Subunit / Source: (natural) Escherichia coli (E. coli) / Strain: K12
#3: RNA chain Helix 44 of 16S rRNA / Coordinate model: P atoms only


Mass: 31208.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: based on coordinates from 1GIX, 30S Subunit / Source: (natural) Escherichia coli (E. coli) / Strain: K12
#4: RNA chain Helix 69 of 23S rRNA / Coordinate model: P atoms only


Mass: 6077.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: based on coordinates from 1GIY, 50S Subunit / Source: (natural) Escherichia coli (E. coli) / Strain: K12
#5: RNA chain Helix 89 of 23S rRNA / Coordinate model: P atoms only


Mass: 18996.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: based on coordinates from 1GIY, 50S Subunit / Source: (natural) Escherichia coli (E. coli) / Strain: K12
#6: RNA chain Helix 93 of 23S rRNA / Coordinate model: P atoms only


Mass: 8706.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: based on coordinates from 1GIY, 50S Subunit / Source: (natural) Escherichia coli (E. coli) / Strain: K12

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Protein , 2 types, 2 molecules OL

#7: Protein 30S RIBOSOMAL PROTEIN S12 / / Coordinate model: Cα atoms only


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: based on coordinates from 1GIX, 30S Subunit / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: Q5SHN3
#8: Protein 50S ribosomal protein L11 / / Coordinate model: Cα atoms only


Mass: 14980.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: based on coordinates from 1GIY, 50S Subunit / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P29395

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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: 70S ribosomeRibosome / Type: RIBOSOME
Buffer solutionName: polymix buffer / pH: 7.5 / Details: polymix buffer
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Nov 8, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 49696 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2020 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1Omodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: Wiener filtering of 3D-maps
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Reference Bases Alignment / Resolution: 12.8 Å / Num. of particles: 18199 / Actual pixel size: 2.82 Å / Magnification calibration: TMV / Details: SPIDER package / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--Manual
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11GIX

1gix
PDB Unreleased entry

11GIX1PDBexperimental model
21GIY

1giy
PDB Unreleased entry

11GIY2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms257 249 0 0 506

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