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- PDB-4v9j: 70S ribosome translocation intermediate GDPNP-II containing elong... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4v9j | |||||||||
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Title | 70S ribosome translocation intermediate GDPNP-II containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state. | |||||||||
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![]() | RIBOSOME/ANTIBIOTIC / GDPNP / chimeric hybrid state ribosome / translocation intermediate / EF-G / mRNA / tRNA / RIBOSOME-ANTIBIOTIC complex | |||||||||
Function / homology | ![]() ribosome disassembly / translation elongation factor activity / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding ...ribosome disassembly / translation elongation factor activity / large ribosomal subunit / 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 / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhou, J. / Lancaster, L. / Donohue, J.P. / Noller, H.F. | |||||||||
![]() | ![]() Title: Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Authors: Zhou, J. / Lancaster, L. / Donohue, J.P. / Noller, H.F. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 7.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 654.9 KB | Display | |
Data in CIF | ![]() | 967.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4v9kC ![]() 4v9lC ![]() 4v9mC ![]() 2wri ![]() 2wrj ![]() 3f1e ![]() 3f1f S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-30S ribosomal protein ... , 19 types, 38 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...
#1: Protein | Mass: 27116.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 22975.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 16460.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 14298.466 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 11398.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 12606.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 13875.388 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 14207.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | Mass: 9995.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | Mass: 11879.112 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | Mass: 8155.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | Mass: 9006.486 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | Mass: 10907.060 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-RNA chain , 5 types, 10 molecules AACAAVCVAWCWBBDBBADA
#20: RNA chain | Mass: 490593.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #21: RNA chain | Mass: 5907.628 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #22: RNA chain | Mass: 24728.689 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #59: RNA chain | Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #60: RNA chain | Mass: 936302.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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+50S ribosomal protein ... , 34 types, 70 molecules BCDCBDDDBEDEBFDFBGDGBHDHBJDJBKDKBODOBPDPBQDQBRDRBSDSBTDTBUDU...
-Protein / Protein/peptide , 2 types, 4 molecules AYCYAUCU
#23: Protein | Mass: 76547.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #24: Protein/peptide | |
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-Non-polymers , 2 types, 4 molecules ![](data/chem/img/GNP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#61: Chemical | #62: Chemical | |
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-Details
Sequence details | E. COLI NUMBERING IS USED FOR 5S, 16S, AND 23S RIBOSOMAL RNA. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.54 % |
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Crystal grow | Details: 2.9% PEG20000, 2.8% PPG P400, 5.1% PEG550 MME, 200 mM potassium thiocyanate, Tris acetate |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3.86→40 Å / Num. obs: 462446 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 3.8 % / Rsym value: 0.336 / Net I/σ(I): 5.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3F1E, 3F1F, 2WRI, AND 2WRJ Resolution: 3.86→40 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.86→40 Å
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Refine LS restraints |
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