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Yorodumi- PDB-4v47: Real space refined coordinates of the 30S and 50S subunits fitted... -
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-Basic information
Entry | Database: PDB / ID: 4v47 | |||||||||
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Title | Real space refined coordinates of the 30S and 50S subunits fitted into the low resolution cryo-EM map of the EF-G.GTP state of E. coli 70S ribosome | |||||||||
Components |
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Keywords | RIBOSOME / EF-G.GTP-bound state / ratchet-like movement / real-space refinement | |||||||||
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 / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / 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) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.3 Å | |||||||||
Authors | Gao, H. / Sengupta, J. / Valle, M. / Korostelev, A. / Eswar, N. / Stagg, S.M. / Van Roey, P. / Agrawal, R.K. / Harvey, S.T. / Sali, A. ...Gao, H. / Sengupta, J. / Valle, M. / Korostelev, A. / Eswar, N. / Stagg, S.M. / Van Roey, P. / Agrawal, R.K. / Harvey, S.T. / Sali, A. / Chapman, M.S. / Frank, J. | |||||||||
Citation | Journal: Cell / Year: 2003 Title: Study of the structural dynamics of the E coli 70S ribosome using real-space refinement. Authors: Haixiao Gao / Jayati Sengupta / Mikel Valle / Andrei Korostelev / Narayanan Eswar / Scott M Stagg / Patrick Van Roey / Rajendra K Agrawal / Stephen C Harvey / Andrej Sali / Michael S Chapman / Joachim Frank / Abstract: Cryo-EM density maps showing the 70S ribosome of E. coli in two different functional states related by a ratchet-like motion were analyzed using real-space refinement. Comparison of the two resulting ...Cryo-EM density maps showing the 70S ribosome of E. coli in two different functional states related by a ratchet-like motion were analyzed using real-space refinement. Comparison of the two resulting atomic models shows that the ribosome changes from a compact structure to a looser one, coupled with the rearrangement of many of the proteins. Furthermore, in contrast to the unchanged inter-subunit bridges formed wholly by RNA, the bridges involving proteins undergo large conformational changes following the ratchet-like motion, suggesting an important role of ribosomal proteins in facilitating the dynamics of translation. #1: Journal: Cell(Cambridge,Mass.) / Year: 2000 Title: Solution structure of the E. coli 70S ribosome at 11.5 A resolution Authors: Gabashvili, I.S. / Agrawal, R.K. / Spahn, C.M.T. / Grassucci, R. / Svergun, D.I. / Frank, J. / Penczek, P. #2: Journal: Nature / Year: 2000 Title: A ratchet-like inter-subunit reorganization of the ribosome during translocation Authors: Frank, J. / Agrawal, R.K. | |||||||||
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 | 4v47.cif.gz | 320.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v47.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v47_validation.pdf.gz | 511.8 KB | Display | wwPDB validaton report |
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Full document | 4v47_full_validation.pdf.gz | 512.1 KB | Display | |
Data in XML | 4v47_validation.xml.gz | 1.2 KB | Display | |
Data in CIF | 4v47_validation.cif.gz | 75.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/4v47 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/4v47 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules A0A9BA
#1: RNA chain | Mass: 941612.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: EMBL: 2073407 |
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#2: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: EMBL: 42753 |
#28: RNA chain | Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: EMBL: V00348 |
+50S ribosomal protein ... , 25 types, 25 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAQARASATAUAWAXAZA1A4
-30S RIBOSOMAL PROTEIN ... , 18 types, 18 molecules BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBT
#29: Protein | Mass: 25900.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7V3 |
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#30: Protein | Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7V8 |
#31: Protein | Mass: 17498.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7W1 |
#32: Protein | Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02358 |
#33: Protein | Mass: 19923.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02359 |
#34: Protein | Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7W7 |
#35: Protein | Mass: 14755.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7X3 |
#36: Protein | Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7R5 |
#37: Protein | Mass: 13739.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7R9 |
#38: Protein | Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7S3 |
#39: Protein | Mass: 12997.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7S9 |
#40: Protein | Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02370, UniProt: P0AG60*PLUS |
#41: Protein | Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02371, UniProt: P0ADZ4*PLUS |
#42: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7T3 |
#43: Protein | Mass: 9593.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02373, UniProt: P0AG66*PLUS |
#44: Protein | Mass: 8874.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7T7 |
#45: Protein | Mass: 10324.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7U3 |
#46: Protein | Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7U7 |
-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: E. coli 70S ribosome -EF-G.GTP complex / Type: RIBOSOME |
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Buffer solution | Name: Tris / pH: 7.5 / Details: Tris |
Specimen | Conc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Details: Rapid-freezing in liquid ethane |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Jan 15, 2001 |
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: 49696 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm |
Specimen holder | Temperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: CTF correction of 3D-maps | |||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Method: Reference based alignment / Resolution: 12.3 Å / Nominal pixel size: 2.8 Å / Actual pixel size: 2.82 Å / Magnification calibration: TMV / Details: SPIDER package / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Target criteria: cross-correlation coefficient, real space R factor Details: METHOD--auto REFINEMENT PROTOCOL--Multi-rigid body, real-space refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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