EMD-11279 Experiments and Validation

Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA

Single particle reconstruction
Overview of EMD-11279
Sample name: Ribosome with mRNA and tRNAs
Organisms: Homo sapiens, Human
Fitted atomic model: 6zm6
Related EM entry by publication: EMD-11278

Map parameters

Recommended contour level: 2.50 (author)
Number of grid points: 540 × 540 × 540
Voxel size: 0.83 × 0.83 × 0.83 Å
Minimum density: -20.948
Maximum density: 55.214
Average density: 0.006
Standard deviation: 1.001

Sample information

Sample name: Ribosome with mRNA and tRNAs
Ligands: MAGNESIUM ION, POTASSIUM ION, ZINC ION, FE2/S2 (INORGANIC) CLUSTER, ADENOSINE-5'-TRIPHOSPHATE, GUANOSINE-5'-TRIPHOSPHATE, water
Nucleic acids: 16S mitochondrial rRNA, mitochondrial tRNAVal, 12S mitochondrial rRNA, A-site tRNA, P-site tRNA, mRNA
Proteins: Ribosome with mRNA and tRNAs, Large subunit of ribosome, Small subunit of ribosome, 39S ribosomal protein L2, mitochondrial, 39S ribosomal protein L3, mitochondrial, 39S ribosomal protein L4, mitochondrial, 39S ribosomal protein L9, mitochondrial, 39S ribosomal protein L10, mitochondrial, 39S ribosomal protein L11, mitochondrial, 39S ribosomal protein L13, mitochondrial, 39S ribosomal protein L14, mitochondrial, 39S ribosomal protein L15, mitochondrial, 39S ribosomal protein L16, mitochondrial, 39S ribosomal protein L17, mitochondrial, 39S ribosomal protein L18, mitochondrial, 39S ribosomal protein L19, mitochondrial, 39S ribosomal protein L20, mitochondrial, 39S ribosomal protein L21, mitochondrial, 39S ribosomal protein L22, mitochondrial, 39S ribosomal protein L23, mitochondrial, 39S ribosomal protein L24, mitochondrial, 39S ribosomal protein L27, mitochondrial, 39S ribosomal protein L28, mitochondrial, 39S ribosomal protein L47, mitochondrial, 39S ribosomal protein L30, mitochondrial, 39S ribosomal protein L32, mitochondrial, 39S ribosomal protein L33, mitochondrial, 39S ribosomal protein L34, mitochondrial, 39S ribosomal protein L35, mitochondrial, 39S ribosomal protein L36, mitochondrial, 39S ribosomal protein L37, mitochondrial, 39S ribosomal protein L38, mitochondrial, 39S ribosomal protein L39, mitochondrial, 39S ribosomal protein L40, mitochondrial, 39S ribosomal protein L41, mitochondrial, 39S ribosomal protein L42, mitochondrial, 39S ribosomal protein L43, mitochondrial, 39S ribosomal protein L44, mitochondrial, 39S ribosomal protein L45, mitochondrial, 39S ribosomal protein L46, mitochondrial, 39S ribosomal protein L48, mitochondrial, 39S ribosomal protein L49, mitochondrial, 39S ribosomal protein L50, mitochondrial, 39S ribosomal protein L51, mitochondrial, 39S ribosomal protein L52, mitochondrial, 39S ribosomal protein L53, mitochondrial, 39S ribosomal protein L54, mitochondrial, 39S ribosomal protein L55, mitochondrial, Ribosomal protein 63, mitochondrial, Peptidyl-tRNA hydrolase ICT1, mitochondrial, Growth arrest and DNA damage-inducible proteins-interacting protein 1, 39S ribosomal protein S18a, mitochondrial, 39S ribosomal protein S30, mitochondrial, 39S ribosomal protein L12, mitochondrial, 28S ribosomal protein S2, mitochondrial, 28S ribosomal protein S24, mitochondrial, 28S ribosomal protein S5, mitochondrial, 28S ribosomal protein S6, mitochondrial, 28S ribosomal protein S7, mitochondrial, 28S ribosomal protein S9, mitochondrial, 28S ribosomal protein S10, mitochondrial, 28S ribosomal protein S11, mitochondrial, 28S ribosomal protein S12, mitochondrial, 28S ribosomal protein S14, mitochondrial, 28S ribosomal protein S15, mitochondrial, 28S ribosomal protein S16, mitochondrial, 28S ribosomal protein S17, mitochondrial, 28S ribosomal protein S18b, mitochondrial, 28S ribosomal protein S18c, mitochondrial, 28S ribosomal protein S21, mitochondrial, 28S ribosomal protein S22, mitochondrial, 28S ribosomal protein S23, mitochondrial, 28S ribosomal protein S25, mitochondrial, 28S ribosomal protein S26, mitochondrial, 28S ribosomal protein S27, mitochondrial, 28S ribosomal protein S28, mitochondrial, 28S ribosomal protein S29, mitochondrial, 28S ribosomal protein S31, mitochondrial, 28S ribosomal protein S33, mitochondrial, 28S ribosomal protein S34, mitochondrial, 28S ribosomal protein S35, mitochondrial, Coiled-coil-helix-coiled-coil-helix domain-containing protein 1, Aurora kinase A-interacting protein, Pentatricopeptide repeat domain-containing protein 3, mitochondrial

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: RELION
Number of particles: 93615

Fitting

Initial atomic models: 3J9M, 5OOL, 6RW4
Target criteria: Correlation coefficient
Overall B value: 44.0
Refinement space: REAL

Imaging

Session
Microscope model: FEI TITAN KRIOS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 30.0
Energy filter: GIF Quantum LS
Nominal CS (mm): 2.70
Nominal magnification: 165000.0
Holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Acquisition
Number of images: 19655

Specimen

Preparation
Specimen state: particle
Vitrification
Apparatus: FEI VITROBOT MARK IV
Cryogen: ETHANE
Humidity: 100