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- PDB-1mj1: FITTING THE TERNARY COMPLEX OF EF-Tu/tRNA/GTP AND RIBOSOMAL PROTE... -

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Basic information

Entry
Database: PDB / ID: 1mj1
TitleFITTING THE TERNARY COMPLEX OF EF-Tu/tRNA/GTP AND RIBOSOMAL PROTEINS INTO A 13 A CRYO-EM MAP OF THE COLI 70S RIBOSOME
Components
  • Elongation Factor TuEF-Tu
  • L11 ribosomal protein
  • Phe-tRNA
  • S12 ribosomal protein
  • S13 ribosomal protein
  • helix 69 of 23S rRNA
  • sarcin-ricin loop of 23SrRNA
KeywordsRIBOSOME / 70S RIBOSOME / LOW RESOLUTION MODEL TERNARY COMPLEX / EF-Tu
Function / homology
Function and homology information


misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic large ribosomal subunit ...misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / GTPase activity / GTP binding / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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 S13, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13-like, H2TH / Ribosomal protein S13 signature. / Ribosomal protein S13 family profile. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Small GTP-binding protein domain / Ribosomal protein S12 signature. / Translation protein, beta-barrel domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS13 / Elongation factor Tu / Small ribosomal subunit protein uS12
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13 Å
AuthorsStark, H. / Rodnina, M.V. / Wieden, H.-J. / Zemlin, F. / Wintermeyer, W. / Vanheel, M.
CitationJournal: Nat Struct Biol / Year: 2002
Title: Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
Authors: Holger Stark / Marina V Rodnina / Hans-Joachim Wieden / Friedrich Zemlin / Wolfgang Wintermeyer / Marin van Heel /
Abstract: The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional ...The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional reconstruction determined by cryo-electron microscopy of the kirromycin-stalled codon-recognition complex. The structure of the ternary complex is distorted by binding of the tRNA anticodon arm in the decoding center. The aa-tRNA interacts with 16S rRNA, helix 69 of 23S rRNA and proteins S12 and L11, while the sarcin-ricin loop of 23S rRNA contacts domain 1 of EF-Tu near the nucleotide-binding pocket. These results provide a detailed snapshot view of an important functional state of the ribosome and suggest mechanisms of decoding and GTPase activation.
History
DepositionAug 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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 ...Data collection / Database references / Derived calculations / 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 / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

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Assembly

Deposited unit
D: Phe-tRNA
C: Phe-tRNA
Q: sarcin-ricin loop of 23SrRNA
R: helix 69 of 23S rRNA
A: Elongation Factor Tu
O: S12 ribosomal protein
P: S13 ribosomal protein
L: L11 ribosomal protein


Theoretical massNumber of molelcules
Total (without water)162,2748
Polymers162,2748
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 , 3 types, 4 molecules DCQR

#1: RNA chain Phe-tRNA


Mass: 24890.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRIES 1GIX, 1TRA / Source: (natural) Escherichia coli (E. coli)
#2: RNA chain sarcin-ricin loop of 23SrRNA / Coordinate model: P atoms only


Mass: 13369.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRY 1GIY / Source: (natural) Escherichia coli (E. coli)
#3: RNA chain helix 69 of 23S rRNA / Coordinate model: P atoms only


Mass: 8688.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRY 1GIY / Source: (natural) Escherichia coli (E. coli)

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Protein , 4 types, 4 molecules AOPL

#4: Protein Elongation Factor Tu / EF-Tu


Mass: 46064.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRY 1B23 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q01698*PLUS
#5: Protein S12 ribosomal protein / Coordinate model: Cα atoms only


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRY 1GIX / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3, UniProt: Q5SHN3*PLUS
#6: Protein S13 ribosomal protein / Coordinate model: Cα atoms only


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRY 1GIX / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P80377*PLUS
#7: Protein L11 ribosomal protein / Coordinate model: Cα atoms only


Mass: 15111.923 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRY 1GIY / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P29395*PLUS

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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: EF-Tu/tRNA/GTP E. COLI 70S RIBOSOME / Type: RIBOSOME
Buffer solutionName: Tris-HClTris / pH: 7.5 / Details: Tris-HCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE
Crystal grow
*PLUS
Method: cryo-electron microscopy / Details: cryo-electron microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG/SOPHIE / Date: Mar 10, 2000
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 58500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 1.35 mm
Specimen holderTemperature: 4.2 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

Software
NameVersionClassification
EMREFINEMENT SOFTWARE PACKAGES : IMAGIC-5refinement
AMIRArefinement
SITUSRECONSTRUCTION SCHEMA : EXACT FILTER BACKPROJECTIONrefinement
IMAGIC-5refinement
EM software
IDNameCategory
1Situsmodel fitting
2IMAGIC3D reconstruction
3Amiramodel fitting
CTF correctionDetails: phase flip
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: "exact filter" backprojection / Resolution: 13 Å / Num. of particles: 24000 / Actual pixel size: 2.25 Å / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Target criteria: best visual fit using the program Amira (ribosomal proteins), best fit using the program Situs (EF-Tu)
Details: REFINEMENT PROTOCOL--rigid body DETAILS--FOR S12, S13, SRL, HELIX69 ANS L11 ONLY BACKBONE COORDINATES ARE DEPOSITED
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11B23

1b23

11B231PDBexperimental model
21GIX

1gix
PDB Unreleased entry

11GIX2PDBexperimental model
31GIY

1giy
PDB Unreleased entry

11GIY3PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 3372 0 0 5374

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