+Open data
-Basic information
Entry | Database: PDB / ID: 8qrm | ||||||
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Title | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 3 | ||||||
Components |
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Keywords | RIBOSOME / Mitochondria / Assembly / GTPBP8 | ||||||
Function / homology | Function and homology information mitochondrial translational initiation / mitochondrial ribosome binding / translation factor activity, RNA binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / ribosome disassembly / negative regulation of mitotic nuclear division ...mitochondrial translational initiation / mitochondrial ribosome binding / translation factor activity, RNA binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / ribosome disassembly / 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 / translation initiation factor activity / apoptotic signaling pathway / fibrillar center / cell junction / ribosome binding / 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 / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å | ||||||
Authors | Valentin Gese, G. / Cipullo, M. / Rorbach, J. / Hallberg, B.M. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: GTPBP8 plays a role in 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qrm.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8qrm.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 8qrm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qrm_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8qrm_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8qrm_validation.xml.gz | 179.3 KB | Display | |
Data in CIF | 8qrm_validation.cif.gz | 283.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/8qrm ftp://data.pdbj.org/pub/pdb/validation_reports/qr/8qrm | HTTPS FTP |
-Related structure data
Related structure data | 18440MC 8qrnC 8qu1C 8qu5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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) Homo sapiens (human) / Cell line: HEK293T / References: GenBank: OM714795.1 |
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+28S ribosomal protein ... , 27 types, 27 molecules BCDEFGHIJKLMNOPQRSTUVWXYZ01
-Protein , 4 types, 4 molecules 2348
#29: Protein | Mass: 13409.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q96BP2 |
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#30: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9NWT8 |
#31: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q96EY7 |
#32: Protein | Mass: 32545.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTIF3, DC38 / Plasmid: pET-24b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q9H2K0 |
-Non-polymers , 9 types, 84 molecules
#33: Chemical | ChemComp-NAD / | ||||||||||
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#34: Chemical | ChemComp-SPM / | ||||||||||
#35: Chemical | ChemComp-SRY / | ||||||||||
#36: Chemical | ChemComp-MG / #37: Chemical | ChemComp-K / #38: Chemical | ChemComp-ZN / | #39: Chemical | #40: Chemical | ChemComp-ATP / | #41: Chemical | ChemComp-GNP / | |
-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 |
-Sample preparation
Component | Name: mtSSU (State 3) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#32 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
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 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
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) |
-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: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73449 / Symmetry type: POINT |