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Yorodumi- PDB-1zo1: IF2, IF1, and tRNA fitted to cryo-EM data OF E. COLI 70S initiati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zo1 | ||||||
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Title | IF2, IF1, and tRNA fitted to cryo-EM data OF E. COLI 70S initiation complex | ||||||
Components |
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Keywords | translation/RNA / E. COLI / RIBOSOME / INITIATION OF PROTEIN SYNTHESIS / INITIATION FACTOR / CRYO-ELETRON MICROSCOPY / translation-RNA COMPLEX | ||||||
Function / homology | Function and homology information guanosine tetraphosphate binding / ribosomal small subunit binding / chaperone-mediated protein folding / translation initiation factor activity / response to cold / translational initiation / ribosome binding / rRNA binding / GTPase activity / GTP binding ...guanosine tetraphosphate binding / ribosomal small subunit binding / chaperone-mediated protein folding / translation initiation factor activity / response to cold / translational initiation / ribosome binding / rRNA binding / GTPase activity / GTP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.8 Å | ||||||
Authors | Allen, G.S. / Zavialov, A. / Gursky, R. / Ehrenberg, M. / Frank, J. | ||||||
Citation | Journal: Cell / Year: 2005 Title: The cryo-EM structure of a translation initiation complex from Escherichia coli. Authors: Gregory S Allen / Andrey Zavialov / Richard Gursky / Måns Ehrenberg / Joachim Frank / Abstract: The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex ...The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex (IC) stalled after 70S assembly. We have obtained a cryo-EM reconstruction of the IC showing IF2*GDPNP at the intersubunit cleft of the 70S ribosome. IF2*GDPNP contacts the 30S and 50S subunits as well as fMet-tRNA(fMet). IF2 here adopts a conformation radically different from that seen in the recent crystal structure of IF2. The C-terminal domain of IF2 binds to the single-stranded portion of fMet-tRNA(fMet), thereby forcing the tRNA into a novel orientation at the P site. The GTP binding domain of IF2 binds to the GTPase-associated center of the 50S subunit in a manner similar to EF-G and EF-Tu. Additionally, we present evidence for the localization of IF1, IF3, one C-terminal domain of L7/L12, and the N-terminal domain of IF2 in the initiation complex. | ||||||
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 | 1zo1.cif.gz | 158.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zo1.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 1zo1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zo1_validation.pdf.gz | 648.9 KB | Display | wwPDB validaton report |
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Full document | 1zo1_full_validation.pdf.gz | 768.2 KB | Display | |
Data in XML | 1zo1_validation.xml.gz | 33.5 KB | Display | |
Data in CIF | 1zo1_validation.cif.gz | 50.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/1zo1 ftp://data.pdbj.org/pub/pdb/validation_reports/zo/1zo1 | HTTPS FTP |
-Related structure data
Related structure data | 1248MC 1249MC 1zo3C 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
#1: RNA chain | Mass: 24518.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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#2: Protein | Mass: 54209.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A705 |
#3: Protein | Mass: 8116.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P69222 |
-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: 70S INITIATION COMPLEX / Type: RIBOSOME Details: 70S E. coli ribosomes, IF1, IF2(GDPNP), IF3, mRNA, and fMet-tRNAfmet formed in vitro |
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Buffer solution | Name: POLYMIX BUFFER / pH: 7.5 / Details: POLYMIX BUFFER |
Specimen | Conc.: 0.032 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE Details: HOLEY CARBON GRID AT 20C FLASH FROZEN INTO LIQUID ETHAN |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Jan 1, 2004 / Details: LOW DOSE MODE |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Nominal defocus max: -3930 nm / Nominal defocus min: -930 nm / Cs: 2 mm |
Specimen holder | Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Film or detector model: KODAK SO-163 FILM |
-Processing
CTF correction | Details: DEFOCUS GROUPS 0.93-3.93 UM | |||||||||||||||||||||
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Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Method: MULTI-REFERENCE / Resolution: 13.8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 20283 / Nominal pixel size: 2.82 Å / Actual pixel size: 2.82 Å Details: resolution 13.8 ANGSTROMS (FSC=0.5) and 8.6 ANGSTROMS (3sigma) Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: BEST FIT USING RSREF Details: METHOD--COORDINATE FILES WERE FITTED TO THE E. COLI TRANSLATION INITIATION COMPLEX MAP (EMBL-EMD 3525). REFINEMENT PROTOCOL--RIGID BODY FIT OF DOMAINS I-V OF IF2, RIGID BODY FIT OF IF1 AND FMET-TRNA | |||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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