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Yorodumi- PDB-4v48: Real space refined coordinates of the 30S and 50S subunits fitted... -
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-Basic information
Entry | Database: PDB / ID: 4v48 | |||||||||
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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 initiation-like 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 / mRNA base-pairing translational repressor activity / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / four-way junction DNA binding ...stringent response / mRNA base-pairing translational repressor activity / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / DNA endonuclease activity / : / cytosolic ribosome assembly / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.5 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 | 4v48.cif.gz | 332.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v48.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/4v48 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/4v48 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 4 types, 4 molecules A0A9A6BA
#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 |
#3: RNA chain | Mass: 24518.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 |
#29: RNA chain | Mass: 499995.156 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 ... , 19 types, 19 molecules BBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBT
#30: Protein | Mass: 26650.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02351, UniProt: P0A7V1*PLUS |
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#31: 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: P02352, UniProt: P0A7V5*PLUS |
#32: 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: P02354, UniProt: P0A7W0*PLUS |
#33: 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: P02356, UniProt: P0A7W2*PLUS |
#34: 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 |
#35: 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 |
#36: 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: P02361, UniProt: P0A7X0*PLUS |
#37: 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: P02363, UniProt: P0A7X3*PLUS |
#38: 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: P02364, UniProt: P0A7R6*PLUS |
#39: 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: P02366, UniProt: P0A7S1*PLUS |
#40: 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: P02367, UniProt: P0A7S4*PLUS |
#41: 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: P02369, UniProt: P0A7T0*PLUS |
#42: 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 |
#43: 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 |
#44: 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: P02372, UniProt: P0A7T3*PLUS |
#45: 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 |
#46: 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: P02374, UniProt: P0A7U2*PLUS |
#47: 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: P02375, UniProt: P0A7U3*PLUS |
#48: 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: P02378, UniProt: P0A7U8*PLUS |
-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 bound with formyl-methionyl initiator tRNA Type: RIBOSOME |
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Buffer solution | Name: hepes / pH: 7.5 / Details: hepes |
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: Jul 1, 1997 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 51200 X / Calibrated magnification: 51200 X / Nominal defocus max: 4340 nm / Nominal defocus min: 730 nm / Cs: 2 mm |
Specimen holder | Temperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 10 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: 11.5 Å / Nominal pixel size: 2.93 Å / Actual pixel size: 2.93 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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