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- PDB-2vrh: Structure of the E. coli trigger factor bound to a translating ri... -

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Basic information

Entry
Database: PDB / ID: 2vrh
TitleStructure of the E. coli trigger factor bound to a translating ribosome
Components
  • 50S RIBOSOMAL PROTEIN L23
  • 50S RIBOSOMAL PROTEIN L24
  • 50S RIBOSOMAL PROTEIN L29
  • TRIGGER FACTOR
KeywordsRIBOSOME / TRIGGER FACTOR / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / CO-TRANSLATIONAL PROTEIN FOLDING / ROTAMASE / CHAPERONE / ISOMERASE / CELL CYCLE / RNA-BINDING / RRNA-BINDING / CELL DIVISION / RIBOSOME-NASCENT CHAIN COMPLEX
Function / homology
Function and homology information


'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / : / protein folding chaperone / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein transport ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / : / protein folding chaperone / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein transport / ribosome binding / response to heat / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cell division / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase ...Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / : / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L24 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L26/L24, KOW domain / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL29 / Trigger factor / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 19 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D
AuthorsMerz, F. / Boehringer, D. / Schaffitzel, C. / Preissler, S. / Hoffmann, A. / Maier, T. / Rutkowska, A. / Lozza, J. / Ban, N. / Bukau, B. / Deuerling, E.
CitationJournal: EMBO J / Year: 2008
Title: Molecular mechanism and structure of Trigger Factor bound to the translating ribosome.
Authors: Frieder Merz / Daniel Boehringer / Christiane Schaffitzel / Steffen Preissler / Anja Hoffmann / Timm Maier / Anna Rutkowska / Jasmin Lozza / Nenad Ban / Bernd Bukau / Elke Deuerling /
Abstract: Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions ...Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions of Escherichia coli TF and nascent chains during translation. Furthermore, we provide the first full-length structure of TF associated with ribosome-nascent chain complexes by using cryo-electron microscopy. In its active state, TF arches over the ribosomal exit tunnel accepting nascent chains in a protective void. The growing nascent chain initially follows a predefined path through the entire interior of TF in an unfolded conformation, and even after folding into a domain it remains accommodated inside the protective cavity of ribosome-bound TF. The adaptability to accept nascent chains of different length and folding states may explain how TF is able to assist co-translational folding of all kinds of nascent polypeptides during ongoing synthesis. Moreover, we suggest a model of how TF's chaperoning function can be coordinated with the co-translational processing and membrane targeting of nascent polypeptides by other ribosome-associated factors.
History
DepositionApr 7, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Derived calculations / Other / Version format compliance
Revision 1.2Aug 7, 2013Group: Other / Refinement description
Revision 1.3Aug 23, 2017Group: Data collection / Refinement description
Category: em_3d_fitting / em_image_scans ...em_3d_fitting / em_image_scans / em_imaging / em_software
Item: _em_3d_fitting.target_criteria / _em_imaging.nominal_defocus_max ..._em_3d_fitting.target_criteria / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _em_software.fitting_id / _em_software.image_processing_id
Revision 1.4May 8, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details

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Assembly

Deposited unit
A: TRIGGER FACTOR
B: 50S RIBOSOMAL PROTEIN L23
C: 50S RIBOSOMAL PROTEIN L24
D: 50S RIBOSOMAL PROTEIN L29


Theoretical massNumber of molelcules
Total (without water)78,4884
Polymers78,4884
Non-polymers00
Water00
1


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

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Components

#1: Protein TRIGGER FACTOR / Coordinate model: Cα atoms only


Mass: 48771.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BASED ON PDB 1W26_A. RESIDUES 22-62 WERE REPLACED WITH THE CORRESPONDING RESIDUES OF PDB 1OMS_B
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: BASED ON PDB 1W26_A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A850
#2: Protein 50S RIBOSOMAL PROTEIN L23 / Coordinate model: Cα atoms only


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BASED ON PDB 2AW4_T / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: Q0TCE3, UniProt: P0ADZ0*PLUS
#3: Protein 50S RIBOSOMAL PROTEIN L24 / Coordinate model: Cα atoms only


Mass: 11208.054 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-104 / Source method: isolated from a natural source / Details: BASED ON PDB 2AW4_U / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P60624
#4: Protein 50S RIBOSOMAL PROTEIN L29 / Coordinate model: Cα atoms only


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BASED ON PDB 2AW4_X / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7M6
Has protein modificationN

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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: STRUCTURE OF THE E. COLI TRIGGER FACTOR BOUND TO A TRANSLATING RIBOSOME
Type: RIBOSOME
Buffer solutionName: 50 MM HEPES-KOH PH 7.5, 100 MM KCL, 25 MM MGCL2, 0.5 MG/ML CHLORAMPHENICOL
pH: 7.5
Details: 50 MM HEPES-KOH PH 7.5, 100 MM KCL, 25 MM MGCL2, 0.5 MG/ML CHLORAMPHENICOL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Specimen holderTemperature: 88 K
Image recordingFilm or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1MOLREPmolecular replacement
2IMAGIC53D reconstruction
3SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: ANGULAR RECONSTITUTION / Resolution: 19 Å / Nominal pixel size: 4.233 Å / Actual pixel size: 4.233 Å / Details: FITTING OF CRYSTAL STRUCTURES INTO MAP EMD-1499 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: REFINEMENT PROTOCOL--RIGID BODY
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12AW4

2aw4
PDB Unreleased entry

12AW41PDBexperimental model
21W26

1w26

11W262PDBexperimental model
RefinementHighest resolution: 19 Å
Refinement stepCycle: LAST / Highest resolution: 19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms695 0 0 0 695

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