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Open data
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Basic information
Entry | Database: PDB / ID: 8qrl | ||||||
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Title | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2 | ||||||
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![]() | RIBOSOME / Mitochondria / Assembly / GTPBP8 | ||||||
Function / homology | ![]() rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial ribosome binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / rRNA base methylation / negative regulation of mitotic nuclear division / mitochondrial small ribosomal subunit ...rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial ribosome binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / rRNA base methylation / negative regulation of mitotic nuclear division / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / Mitochondrial protein degradation / Transferases; Transferring one-carbon groups; Methyltransferases / apoptotic signaling pathway / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / nuclear membrane / cytosolic small ribosomal subunit / cell population proliferation / mitochondrial inner membrane / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleolus / GTP binding / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å | ||||||
![]() | Valentin Gese, G. / Cipullo, M. / Rorbach, J. / Hallberg, B.M. | ||||||
Funding support | 1items
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![]() | ![]() Title: GTPBP8 is essential for mitoribosome formation in human mitochondria Authors: Cipullo, M. / Valentin Gese, G. / Gopalakrishna, S. / Krueger, A. / Lobo, V. / Pirozhkova, M.A. / Marks, J. / Palenkova, P. / Shiriaev, D. / Liu, Y. / Misic, J. / Cai, Y. / Nguyen, M. / ...Authors: Cipullo, M. / Valentin Gese, G. / Gopalakrishna, S. / Krueger, A. / Lobo, V. / Pirozhkova, M.A. / Marks, J. / Palenkova, P. / Shiriaev, D. / Liu, Y. / Misic, J. / Cai, Y. / Nguyen, M. / Abdelbagi, A. / Li, X. / Minczuk, M. / Hafner, M. / Benhalevy, D. / Sarshad, A.A. / Attanasov, I. / Hallberg, B.M. / Rorbach, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 173 KB | Display | |
Data in CIF | ![]() | 285.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18439MC ![]() 8qrkC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 306547.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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+28S ribosomal protein ... , 27 types, 27 molecules BCDEFGHIJKLMNOPQRSTUVWXYZ01
-Protein , 3 types, 3 molecules 348
#29: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#30: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#31: Protein | Mass: 46184.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: A6NJ78, Transferases; Transferring one-carbon groups; Methyltransferases |
-Non-polymers , 9 types, 2239 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
#32: Chemical | ChemComp-NAD / | ||||||||||||||
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#33: Chemical | ChemComp-MG / #34: Chemical | ChemComp-K / #35: Chemical | ChemComp-ZN / | #36: Chemical | #37: Chemical | ChemComp-ATP / | #38: Chemical | ChemComp-GDP / | #39: Chemical | ChemComp-SAH / | #40: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: mtSSU assembly intermediate (State 2) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#31 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
EM embedding | Material: Ice |
Vitrification | Cryogen name: ETHANE |
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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 defocus max: 3000 nm / Nominal defocus min: 200 nm |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software | Name: cryoSPARC / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 435172 |
3D reconstruction | Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32577 / Symmetry type: POINT |