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Yorodumi- PDB-5imq: Structure of ribosome bound to cofactor at 3.8 angstrom resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 5imq | ||||||
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Title | Structure of ribosome bound to cofactor at 3.8 angstrom resolution | ||||||
Components |
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Keywords | RIBOSOME / EF4/LepA / translational GTPase factors / translocation / reverse | ||||||
Function / homology | Function and homology information : / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / positive regulation of translation / large ribosomal subunit / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...: / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / positive regulation of translation / large ribosomal subunit / 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 / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Kumar, V. / Ero, R. / Jian, G.K. / Ahmed, T. / Zhan, Y. / Bhushan, S. / Gao, Y.G. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: J Biol Chem / Year: 2016 Title: Structure of the GTP Form of Elongation Factor 4 (EF4) Bound to the Ribosome. Authors: Veerendra Kumar / Rya Ero / Tofayel Ahmed / Kwok Jian Goh / Yin Zhan / Shashi Bhushan / Yong-Gui Gao / Abstract: Elongation factor 4 (EF4) is a member of the family of ribosome-dependent translational GTPase factors, along with elongation factor G and BPI-inducible protein A. Although EF4 is highly conserved in ...Elongation factor 4 (EF4) is a member of the family of ribosome-dependent translational GTPase factors, along with elongation factor G and BPI-inducible protein A. Although EF4 is highly conserved in bacterial, mitochondrial, and chloroplast genomes, its exact biological function remains controversial. Here we present the cryo-EM reconstitution of the GTP form of EF4 bound to the ribosome with P and E site tRNAs at 3.8-Å resolution. Interestingly, our structure reveals an unrotated ribosome rather than a clockwise-rotated ribosome, as observed in the presence of EF4-GDP and P site tRNA. In addition, we also observed a counterclockwise-rotated form of the above complex at 5.7-Å resolution. Taken together, our results shed light on the interactions formed between EF4, the ribosome, and the P site tRNA and illuminate the GTPase activation mechanism at previously unresolved detail. | ||||||
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 | 5imq.cif.gz | 3.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5imq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5imq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5imq_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5imq_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5imq_validation.xml.gz | 229 KB | Display | |
Data in CIF | 5imq_validation.cif.gz | 396.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/5imq ftp://data.pdbj.org/pub/pdb/validation_reports/im/5imq | HTTPS FTP |
-Related structure data
Related structure data | 6584MC 6585C 5imrC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+50S ribosomal protein ... , 30 types, 30 molecules 123Zabcdefghijklmnopqrstuvwxyz
-RNA chain , 5 types, 5 molecules 45ADE
#4: RNA chain | Mass: 24802.785 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389 (bacteria) References: GenBank: 998643509 |
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#5: RNA chain | Mass: 24485.539 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389 (bacteria) References: GenBank: 998643509 |
#6: RNA chain | Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 55771382 |
#7: RNA chain | Mass: 940788.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 55771382 |
#8: RNA chain | Mass: 39846.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 55771382 |
-30S ribosomal protein ... , 20 types, 20 molecules FGHIJKLMNOPQRSTUVWXY
#9: Protein | Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371 |
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#10: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372 |
#11: Protein | Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373 |
#12: Protein | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5 |
#13: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8 |
#14: Protein | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291 |
#15: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS |
#16: Protein | Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374 |
#17: Protein | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7 |
#18: Protein | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376 |
#19: Protein | Mass: 14637.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3 |
#20: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377 |
#21: Protein | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS |
#22: Protein | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76 |
#23: Protein | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3 |
#24: Protein | Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P24321 |
#25: Protein | Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80382 |
#26: Protein | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2 |
#27: Protein | Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380 |
#28: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3 |
-Protein / Non-polymers , 2 types, 2 molecules B
#56: Protein | Mass: 67690.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: lepA, TTHA0741 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q5SKA7, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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#57: Chemical | ChemComp-GCP / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 2.5 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) | ||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: Buffer G 5 mM HEPES pH 7.5, 10 mM MgAc, 50 mM KCl, 10 mM NH4Cl, and 6 mM 2-mercaptoethanol | ||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: OTHER / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 22 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
Particle selection | Num. of particles selected: 164338 | |||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110981 / Symmetry type: POINT | |||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||
Atomic model building |
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