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Yorodumi- PDB-3deg: Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3deg | ||||||
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Title | Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP | ||||||
Components |
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Keywords | RIBOSOME / translation / LepA / EF4 / GTP-binding / Membrane / Nucleotide-binding / Antibiotic resistance / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / Methylation | ||||||
Function / homology | Function and homology information : / response to pH / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / ribosomal small subunit binding / translation elongation factor activity ...: / response to pH / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / ribosomal small subunit binding / translation elongation factor activity / translational termination / response to salt stress / response to cold / positive regulation of RNA splicing / ribosomal large subunit assembly / positive regulation of translation / maintenance of translational fidelity / ribosome binding / ribosomal small subunit biogenesis / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / GTP binding / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.9 Å | ||||||
Authors | Connell, S.R. / Topf, M. / Qin, Y. / Wilson, D.N. / Mielke, T. / Fucini, P. / Nierhaus, K.H. / Spahn, C.M.T. | ||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2008 Title: A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation. Authors: Sean R Connell / Maya Topf / Yan Qin / Daniel N Wilson / Thorsten Mielke / Paola Fucini / Knud H Nierhaus / Christian M T Spahn / Abstract: EF4 (LepA) is an almost universally conserved translational GTPase in eubacteria. It seems to be essential under environmental stress conditions and has previously been shown to back-translocate the ...EF4 (LepA) is an almost universally conserved translational GTPase in eubacteria. It seems to be essential under environmental stress conditions and has previously been shown to back-translocate the tRNAs on the ribosome, thereby reverting the canonical translocation reaction. In the current work, EF4 was directly visualized in the process of back-translocating tRNAs by single-particle cryo-EM. Using flexible fitting methods, we built a model of ribosome-bound EF4 based on the cryo-EM map and a recently published unbound EF4 X-ray structure. The cryo-EM map establishes EF4 as a noncanonical elongation factor that interacts not only with the elongating ribosome, but also with the back-translocated tRNA in the A-site region, which is present in a previously unseen, intermediate state and deviates markedly from the position of a canonical A-tRNA. Our results, therefore, provide insight into the underlying structural principles governing back-translocation. | ||||||
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 | 3deg.cif.gz | 325.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3deg.ent.gz | 243 KB | Display | PDB format |
PDBx/mmJSON format | 3deg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3deg_validation.pdf.gz | 926.5 KB | Display | wwPDB validaton report |
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Full document | 3deg_full_validation.pdf.gz | 1020.9 KB | Display | |
Data in XML | 3deg_validation.xml.gz | 48.1 KB | Display | |
Data in CIF | 3deg_validation.cif.gz | 70.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/3deg ftp://data.pdbj.org/pub/pdb/validation_reports/de/3deg | HTTPS FTP |
-Related structure data
Related structure data | 1524MC 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 , 2 types, 2 molecules AB
#1: RNA chain | Mass: 24890.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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#2: RNA chain | Mass: 24816.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
-30S RNA helix ... , 2 types, 2 molecules EF
#3: RNA chain | Mass: 5161.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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#4: RNA chain | Mass: 3827.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
-50S RNA helix ... , 4 types, 4 molecules GIJK
#5: RNA chain | Mass: 22580.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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#6: RNA chain | Mass: 9394.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#7: RNA chain | Mass: 5765.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#8: RNA chain | Mass: 4745.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
-Protein , 3 types, 3 molecules CDH
#9: Protein | Mass: 60476.660 Da / Num. of mol.: 1 / Fragment: EF4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lepA, b2569, JW2553 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P60785 |
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#10: Protein | Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7S3 |
#11: Protein | Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7J7 |
-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: Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP Type: COMPLEX |
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Buffer solution | Details: 20 mM HEPES-KOH (pH 7.6), 4.5 mM Mg(CH3COO)2, 150 mM NH4CH3COO, 4 mM B-mercaptoethanol, 2 mM spermidine, and 0.05 mM spermine |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Nominal defocus max: 3900 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 10.9 Å / Num. of particles: 41294 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT Details: REFINEMENT PROTOCOL--rigid body and flexible fitting | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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