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Yorodumi- PDB-3jcn: Structures of ribosome-bound initiation factor 2 reveal the mecha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jcn | ||||||
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Title | Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association: Initiation Complex I | ||||||
Components |
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Keywords | RIBOSOME / translation initiation / GTPase / 70S / bacterial ribosome / IF2 / initiation factor 2 | ||||||
Function / homology | Function and homology information guanosine tetraphosphate binding / stringent response / 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 ...guanosine tetraphosphate binding / stringent response / 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 / four-way junction DNA binding / translational termination / DnaA-L2 complex / chaperone-mediated protein folding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / translation initiation factor activity / 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 / translational initiation / 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 / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||
Authors | Sprink, T. / Ramrath, D.J.F. / Yamamoto, H. / Yamamoto, K. / Loerke, J. / Ismer, J. / Hildebrand, P.W. / Scheerer, P. / Buerger, J. / Mielke, T. / Spahn, C.M.T. | ||||||
Citation | Journal: Sci Adv / Year: 2016 Title: Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association. Authors: Thiemo Sprink / David J F Ramrath / Hiroshi Yamamoto / Kaori Yamamoto / Justus Loerke / Jochen Ismer / Peter W Hildebrand / Patrick Scheerer / Jörg Bürger / Thorsten Mielke / Christian M T Spahn / Abstract: Throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine ...Throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trGTPase). Although the structural basis for trGTPase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with the ribosome, remains elusive. We determine the structure of IF2 complexed with a nonhydrolyzable guanosine triphosphate analog and initiator fMet-tRNAi (Met) in the context of the Escherichia coli ribosome to 3.7-Å resolution using cryo-electron microscopy. The structural analysis reveals previously unseen intrinsic conformational modes of the 70S initiation complex, establishing the mutual interplay of IF2 and initator transfer RNA (tRNA) with the ribsosome and providing the structural foundation for a mechanistic understanding of the final steps of translation initiation. | ||||||
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 | 3jcn.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3jcn.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 3jcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jcn_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 3jcn_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3jcn_validation.xml.gz | 208.8 KB | Display | |
Data in CIF | 3jcn_validation.cif.gz | 363.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/3jcn ftp://data.pdbj.org/pub/pdb/validation_reports/jc/3jcn | HTTPS FTP |
-Related structure data
Related structure data | 3285MC 6559C 3jcjC 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
+50S ribosomal protein ... , 29 types, 29 molecules 01234CDEFGHIJKLMNOPQRSTUVWXYZ
-RNA chain , 5 types, 5 molecules ABavz
#6: RNA chain | Mass: 941612.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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#7: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: U00096.3 |
#32: RNA chain | Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: U00096.3 |
#52: RNA chain | Mass: 24818.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#55: RNA chain | Mass: 1900.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
-Protein , 1 types, 1 molecules b
#33: Protein | Mass: 97498.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: infB, gicD, ssyG, b3168, JW3137 / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A705 |
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-30S ribosomal protein ... , 20 types, 20 molecules cdfghijklmnopqrstuwx
#34: Protein | Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3 |
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#35: Protein | Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0 |
#36: Protein | Mass: 16772.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W1 |
#37: Protein | Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8 |
#38: Protein | Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359 |
#39: Protein | Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358 |
#40: Protein | Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7X3 |
#41: Protein | Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W7 |
#42: Protein | Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9 |
#43: Protein | Mass: 11698.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R5 |
#44: Protein | Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S9 |
#45: Protein | Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3 |
#46: Protein | Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ4 |
#47: Protein | Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG59 |
#48: Protein | Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG63 |
#49: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T3 |
#50: Protein | Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U3 |
#51: Protein | Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T7 |
#53: Protein | Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68679 |
#54: Protein | Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7 |
-Non-polymers , 2 types, 2 molecules
#56: Chemical | ChemComp-GNP / |
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#57: Chemical | ChemComp-FME / |
-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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Buffer solution | Name: 20 mM HEPES-KOH, pH 7.5, 15 mM magnesium acetate, 150 mM potassium acetate, 4 mM 2-mercapthoethanol, 2 mM spermidine, 0.05 mM spermine pH: 7.5 Details: 20 mM HEPES-KOH, pH 7.5, 15 mM magnesium acetate, 150 mM potassium acetate, 4 mM 2-mercapthoethanol, 2 mM spermidine, 0.05 mM spermine | |||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: Quantifoil R3-3 Cu 300 mesh with 2 nm carbon support film | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % Details: Blot for 2-4 seconds before plunging into liquid ethane (FEI VITROBOT MARK I). Method: Blot for 2-4 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company | ||||||||||||||||||
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EM imaging | Accelerating voltage: 300 kV / Calibrated magnification: 39000 X / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: FEI POLARA 300 / Mode: BRIGHT FIELD / Cs: 2 mm / Nominal magnification: 31000 X / Specimen holder type: GATAN LIQUID NITROGEN / Specimen-ID: 1
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Image recording |
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-Processing
EM software |
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CTF correction | Details: CTFFIND4 | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14872 / Nominal pixel size: 1.23 Å / Actual pixel size: 1.23 Å Details: Final maps were calculated from two combined datasets. To avoid overfitting, the data were refined in a resolution-limited scheme using SPIDER. Symmetry type: POINT | ||||||||||||||||||||
Refinement step | Cycle: LAST
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