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- PDB-7unq: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7unq | |||||||||
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Title | Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex, from focused classification and refinement (I-A) | |||||||||
![]() | Translation initiation factor IF-2 | |||||||||
![]() | RIBOSOME / Initiation Factor 2 / 70S ribosome / cryo-EM / translation initiation / initiator tRNA / conformational changes | |||||||||
Function / homology | ![]() translational initiation / translation initiation factor activity / GTPase activity / GTP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Basu, R.S. / Sherman, M.B. / Gagnon, M.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation Authors: Basu, R.S. / Sherman, M.B. / Gagnon, M.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.4 KB | Display | ![]() |
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PDB format | ![]() | 70 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 31.6 KB | Display | |
Data in CIF | ![]() | 42.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26629MC ![]() 7unrC ![]() 7untC ![]() 7unuC ![]() 7unvC ![]() 7unwC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() Data size: 1.7 TB Data #1: Unaligned multiframe micrographs of the Pseudomonas aeruginosa 70S ribosome initiation complex bound to IF2 collected on Gatan K3 in Super Resolution [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 91049.641 Da / Num. of mol.: 1 / Fragment: N2 sub-domain of IF2 Source method: isolated from a genetically manipulated source Details: Initiation Factor 2 / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GDP / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex, from focused classification and refinement (I-A) Type: RIBOSOME / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R2/1 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 295 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 200 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1 sec. / Electron dose: 31 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8056 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 878576 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21480 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3JCJ Accession code: 3JCJ / Source name: PDB / Type: experimental model |