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- PDB-7unw: Pseudomonas aeruginosa 70S ribosome initiation complex bound to I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7unw | |||||||||
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Title | Pseudomonas aeruginosa 70S ribosome initiation complex bound to IF2-GDPCP (structure II-B) | |||||||||
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![]() | RIBOSOME / Initiation Factor 2 / 70S ribosome / cryo-EM / translation initiation / initiator tRNA / conformational changes | |||||||||
Function / homology | ![]() translation initiation factor activity / translational initiation / large ribosomal subunit / 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 ...translation initiation factor activity / translational initiation / large ribosomal subunit / 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 / RNA binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 26635MC ![]() 7unqC ![]() 7unrC ![]() 7untC ![]() 7unuC ![]() 7unvC 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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Components
-RNA chain , 5 types, 5 molecules avwAB
#1: RNA chain | Mass: 497973.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#22: RNA chain | Mass: 24846.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Initiator Methionine tRNA / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#23: RNA chain | Mass: 7804.735 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: IDT-Synthesized 24-nt M-F-Stop mRNA / Source: (synth.) ![]() |
#25: RNA chain | Mass: 937132.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#26: RNA chain | Mass: 38596.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu
#2: Protein | Mass: 27376.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: O82850 |
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#3: Protein | Mass: 25887.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HWE1 |
#4: Protein | Mass: 23318.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: O52759 |
#5: Protein | Mass: 17650.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HWF2 |
#6: Protein | Mass: 16189.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HUM9 |
#7: Protein | Mass: 17541.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HWD1 |
#8: Protein | Mass: 14190.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HWE9 |
#9: Protein | Mass: 14643.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HVY3 |
#10: Protein | Mass: 11786.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HWD4 |
#11: Protein | Mass: 13654.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HWF8 |
#12: Protein | Mass: 13830.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HWD0 |
#13: Protein | Mass: 13292.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HWF7 |
#14: Protein | Mass: 11591.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HWE8 |
#15: Protein | Mass: 10135.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HV58 |
#16: Protein | Mass: 9219.454 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HXP9 |
#17: Protein | Mass: 10106.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HWE4 |
#18: Protein | Mass: 8892.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HUN0 |
#19: Protein | Mass: 10382.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HWD9 |
#20: Protein | Mass: 9942.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9HVM1 |
#21: Protein | Mass: 8508.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9I5V8 |
-Protein , 1 types, 1 molecules x
#24: 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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+50S ribosomal protein ... , 31 types, 31 molecules CDEFGHIJLMNOPQRSTUVWXYZ12345678
-Non-polymers , 5 types, 1152 molecules ![](data/chem/img/MG.gif)
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![](data/chem/img/GCP.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/FME.gif)
![](data/chem/img/GCP.gif)
![](data/chem/img/ZN.gif)
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#58: Chemical | ChemComp-MG / #59: Chemical | ChemComp-FME / | #60: Chemical | ChemComp-GCP / | #61: Chemical | #62: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-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: Pseudomonas aeruginosa 70S ribosome initiation complex bound to IF2-GDPCP (structure II-B) Type: RIBOSOME / Entity ID: #1-#57 / Source: MULTIPLE SOURCES |
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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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98715 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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