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Yorodumi- PDB-4v5h: E.Coli 70s Ribosome Stalled During Translation Of Tnac Leader Peptide. -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v5h | |||||||||
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Title | E.Coli 70s Ribosome Stalled During Translation Of Tnac Leader Peptide. | |||||||||
Components |
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Keywords | RIBOSOME / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / TRANSLATION / ZINC-FINGER / TNAC / 70S RIBOSOME / STALLING | |||||||||
Function / homology | Function and homology information stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||
Authors | Seidelt, B. / Innis, C.A. / Wilson, D.N. / Gartmann, M. / Armache, J. / Villa, E. / Trabuco, L.G. / Becker, T. / Mielke, T. / Schulten, K. ...Seidelt, B. / Innis, C.A. / Wilson, D.N. / Gartmann, M. / Armache, J. / Villa, E. / Trabuco, L.G. / Becker, T. / Mielke, T. / Schulten, K. / Steitz, T.A. / Beckmann, R. | |||||||||
Citation | Journal: Science / Year: 2009 Title: Structural insight into nascent polypeptide chain-mediated translational stalling. Authors: Birgit Seidelt / C Axel Innis / Daniel N Wilson / Marco Gartmann / Jean-Paul Armache / Elizabeth Villa / Leonardo G Trabuco / Thomas Becker / Thorsten Mielke / Klaus Schulten / Thomas A ...Authors: Birgit Seidelt / C Axel Innis / Daniel N Wilson / Marco Gartmann / Jean-Paul Armache / Elizabeth Villa / Leonardo G Trabuco / Thomas Becker / Thorsten Mielke / Klaus Schulten / Thomas A Steitz / Roland Beckmann / Abstract: Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling during translation of the upstream TnaC leader peptide, a process for which interactions between the TnaC nascent ...Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling during translation of the upstream TnaC leader peptide, a process for which interactions between the TnaC nascent chain and the ribosomal exit tunnel are critical. We determined a 5.8 angstrom-resolution cryo-electron microscopy and single-particle reconstruction of a ribosome stalled during translation of the tnaC leader gene. The nascent chain was extended within the exit tunnel, making contacts with ribosomal components at distinct sites. Upon stalling, two conserved residues within the peptidyltransferase center adopted conformations that preclude binding of release factors. We propose a model whereby interactions within the tunnel are relayed to the peptidyltransferase center to inhibit translation. Moreover, we show that nascent chains adopt distinct conformations within the ribosomal exit tunnel. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4v5h.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v5h.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v5h_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4v5h_full_validation.pdf.gz | 5.8 MB | Display | |
Data in XML | 4v5h_validation.xml.gz | 670.6 KB | Display | |
Data in CIF | 4v5h_validation.cif.gz | 923.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/4v5h ftp://data.pdbj.org/pub/pdb/validation_reports/v5/4v5h | HTTPS FTP |
-Related structure data
Related structure data | 1657MC 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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1 |
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-Components
-RNA chain , 5 types, 5 molecules AAAVAXBABB
#1: RNA chain | Mass: 495927.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: GenBank: 54791136 |
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#22: RNA chain | Mass: 24890.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: GenBank: 54791136 |
#23: RNA chain | Mass: 3497.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#34: RNA chain | Mass: 37848.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: GenBank: 38859724 |
#35: RNA chain | Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: GenBank: 38859724 |
-30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU
#2: Protein | Mass: 24253.943 Da / Num. of mol.: 1 / Fragment: RESIDUES 9-226 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7V0 |
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#3: Protein | Mass: 23078.785 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-207 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7V3 |
#4: Protein | Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7V8 |
#5: Protein | Mass: 15804.282 Da / Num. of mol.: 1 / Fragment: RESIDUES 10-159 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7W1 |
#6: Protein | Mass: 11669.371 Da / Num. of mol.: 1 / Fragment: 1-100 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P02358 |
#7: Protein | Mass: 16764.406 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-152 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P02359 |
#8: Protein | Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7W7 |
#9: Protein | Mass: 14554.882 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-130 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7X3 |
#10: Protein | Mass: 11196.988 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-102 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7R5 |
#11: Protein | Mass: 12487.200 Da / Num. of mol.: 1 / Fragment: RESIDUES 13-129 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7R9 |
#12: Protein | Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7S3 |
#13: Protein | Mass: 12528.639 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-114 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7S9 |
#14: Protein | Mass: 11028.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0AG59 |
#15: Protein | Mass: 10188.687 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-89 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: Q8X9M2 |
#16: Protein | Mass: 9065.417 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-80 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7T3 |
#17: Protein | Mass: 9263.946 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-83 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0AG63 |
#18: Protein | Mass: 6466.477 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-74 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7T7 |
#19: Protein | Mass: 9057.626 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-81 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7U3 |
#20: Protein | Mass: 9506.190 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-87 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7U7 |
#21: Protein | Mass: 6067.081 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-54 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P68679 |
-Protein/peptide , 1 types, 1 molecules AZ
#24: Protein/peptide | Mass: 1439.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) |
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+50S RIBOSOMAL PROTEIN ... , 30 types, 30 molecules B0B1B2B3B4B5B6B7B8BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBWBY
-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: TNAC STALLED 70S RIBOSOME WITH P-SITE TRNA. / Type: RIBOSOME |
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Buffer solution | Name: 50 MM TRIS-HCL PH 8.0, 10MM MG-ACETATE, 50MM KCL, 10MM NH4CL, 2MM EGTA, 2MM L-TRYPTOPHAN, 10 MM DTT pH: 8 Details: 50 MM TRIS-HCL PH 8.0, 10MM MG-ACETATE, 50MM KCL, 10MM NH4CL, 2MM EGTA, 2MM L-TRYPTOPHAN, 10 MM DTT |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Cryogen name: ETHANE / Details: CRYOGEN- ETHANE, |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 38900 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.26 mm |
Specimen holder | Temperature: 95 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 128 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: DEFOCUS GROUP VOLUMES | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 5.8 Å / Num. of particles: 263000 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--MDFF REFINEMENT PROTOCOL--FLEXIBLE FITTING | |||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 5.8 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 5.8 Å
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