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Yorodumi- 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 | ||||||
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Title | Structure of the E. coli trigger factor bound to a translating ribosome | ||||||
Components |
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Keywords | RIBOSOME / 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 / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / ribosomal large subunit assembly / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / ribosomal large subunit assembly / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / large ribosomal subunit rRNA binding / response to heat / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / cell division / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 19 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C, D | ||||||
Authors | Merz, F. / Boehringer, D. / Schaffitzel, C. / Preissler, S. / Hoffmann, A. / Maier, T. / Rutkowska, A. / Lozza, J. / Ban, N. / Bukau, B. / Deuerling, E. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2vrh.cif.gz | 36.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vrh.ent.gz | 19 KB | Display | PDB format |
PDBx/mmJSON format | 2vrh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vrh_validation.pdf.gz | 742.5 KB | Display | wwPDB validaton report |
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Full document | 2vrh_full_validation.pdf.gz | 742.1 KB | Display | |
Data in XML | 2vrh_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 2vrh_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/2vrh ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vrh | HTTPS FTP |
-Related structure data
Related structure data | 1499MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 | 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 | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: STRUCTURE OF THE E. COLI TRIGGER FACTOR BOUND TO A TRANSLATING RIBOSOME Type: RIBOSOME |
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Buffer solution | Name: 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 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 20 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm |
Specimen holder | Temperature: 88 K |
Image recording | Film or detector model: KODAK SO-163 FILM |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Method: 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 building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: REFINEMENT PROTOCOL--RIGID BODY | |||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 19 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 19 Å
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