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Yorodumi- PDB-3jcd: Structure of Escherichia coli EF4 in posttranslocational ribosome... -
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-Basic information
Entry | Database: PDB / ID: 3jcd | ||||||
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Title | Structure of Escherichia coli EF4 in posttranslocational ribosomes (Post EF4) | ||||||
Components |
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Keywords | RIBOSOME / ribosome elongation / GTPase EF4 / tRNA back-translocation / P-loop | ||||||
Function / homology | Function and homology information : / response to pH / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding ...: / response to pH / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / ribosomal small subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translation elongation factor activity / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / response to salt stress / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / response to cold / 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 / positive regulation of translation / 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 / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Zhang, D. / Yan, K. / Liu, G. / Song, G. / Luo, J. / Shi, Y. / Cheng, E. / Wu, S. / Jiang, T. / Low, J. ...Zhang, D. / Yan, K. / Liu, G. / Song, G. / Luo, J. / Shi, Y. / Cheng, E. / Wu, S. / Jiang, T. / Low, J. / Gao, N. / Qin, Y. | ||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2016 Title: EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome. Authors: Dejiu Zhang / Kaige Yan / Guangqiao Liu / Guangtao Song / Jiejian Luo / Yi Shi / Erchao Cheng / Shan Wu / Taijiao Jiang / Jizhong Lou / Ning Gao / Yan Qin / Abstract: EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2- ...EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2-Å resolution, respectively. In Post-EF4, peptidyl-tRNA occupies the peptidyl (P) site, but the interaction between its CCA end and the P loop is disrupted. In Pre-EF4, the peptidyl-tRNA assumes a unique position near the aminoacyl (A) site, denoted the A site/EF4 bound (A/4) site, with a large displacement at its acceptor arm. Mutagenesis analyses suggest that a specific region in the EF4 C-terminal domain (CTD) interferes with base-pairing between the peptidyl-tRNA 3'-CCA and the P loop, whereas the EF4 CTD enhances peptidyl-tRNA interaction at the A/4 site. Therefore, EF4 induces back-translocation by disengaging the tRNA's CCA end from the peptidyl transferase center of the translating ribosome. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 3jcd.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3jcd.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 3jcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jcd_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 3jcd_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3jcd_validation.xml.gz | 204.9 KB | Display | |
Data in CIF | 3jcd_validation.cif.gz | 361.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/3jcd ftp://data.pdbj.org/pub/pdb/validation_reports/jc/3jcd | HTTPS FTP |
-Related structure data
Related structure data | 6549MC 6550C 3jceC 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
-30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu
#1: Protein | Mass: 26781.670 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsB, b0169, JW0164 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V0 |
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#2: Protein | Mass: 26031.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsC / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V3 |
#3: Protein | Mass: 23514.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsD, ramA, b3296, JW3258 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V8 |
#4: Protein | Mass: 17629.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsE, spc, b3303, JW3265 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7W1 |
#5: Protein | Mass: 15727.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsF, b4200, JW4158 / Production host: Escherichia coli (E. coli) / References: UniProt: P02358 |
#6: Protein | Mass: 20055.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsG, b3341, JW3303 / Production host: Escherichia coli (E. coli) / References: UniProt: P02359 |
#7: Protein | Mass: 14146.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsH, b3306, JW3268 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7W7 |
#8: Protein | Mass: 14886.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsI, b3230, JW3199 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7X3 |
#9: Protein | Mass: 11755.597 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsJ, nusE, b3321, JW3283 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R5 |
#10: Protein | Mass: 13870.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsK, b3297, JW3259 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R9 |
#11: Protein | Mass: 13768.157 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsL / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7S3 |
#12: Protein | Mass: 13128.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsM, b3298, JW3260 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7S9 |
#13: Protein | Mass: 11606.560 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsN, b3307, JW3269 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG59 |
#14: Protein | Mass: 10290.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsO, secC, b3165, JW3134 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADZ4 |
#15: Protein | Mass: 9207.572 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsP, b2609, JW2590 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7T3 |
#16: Protein | Mass: 9724.491 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsQ, neaA, b3311, JW3273 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG63 |
#17: Protein | Mass: 9005.472 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsR / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7T7 |
#18: Protein | Mass: 10455.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsS, b3316, JW3278 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7U3 |
#19: Protein | Mass: 9708.464 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsT, b0023, JW0022 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7U7 |
#20: Protein | Mass: 8524.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsU / Production host: Escherichia coli (E. coli) / References: UniProt: P68679 |
+50S ribosomal protein ... , 30 types, 30 molecules 012345CDEFGHIJKLMNOPQRSTUVWXYZ
-Protein , 1 types, 1 molecules x
#51: Protein | Mass: 66652.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: lepA, b2569, JW2553 / Production host: Escherichia coli (E. coli) / References: UniProt: P60785, EC: 3.6.5.1 |
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-RNA chain , 5 types, 6 molecules aAB789
#52: RNA chain | Mass: 496892.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) |
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#53: RNA chain | Mass: 941612.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) |
#54: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) |
#55: RNA chain | Mass: 4784.921 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#56: RNA chain | Mass: 24485.539 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-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 |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Oct 20, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
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3D reconstruction | Resolution: 3.7 Å / Num. of particles: 18772 Details: (SINGLE PARTICLE DETAILS: THE PARTICLES WERE SELECTED USING AN AUTOMATIC SELECTION PROGRAM.) (SINGLE PARTICLE- -APPLIED SYMMETRY: C1) Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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