[English] 日本語

- EMDB-4370: Unique features of mammalian mitochondrial translation initiation... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-4370 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 39S ribosomal subunit. | ||||||||||||
![]() | |||||||||||||
![]() |
| ||||||||||||
![]() | translation initiation / initiation factor IF2 / mitochondria / membrane targeting / RIBOSOME | ||||||||||||
Function / homology | ![]() Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / translation factor activity, RNA binding / mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / ribonuclease III activity / translation release factor activity, codon nonspecific / Mitochondrial translation initiation ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / translation factor activity, RNA binding / mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / ribonuclease III activity / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial ribosome / ribosome disassembly / peptidyl-tRNA hydrolase activity / mitochondrial translation / regulation of translational initiation / organelle membrane / ribosomal small subunit binding / RNA processing / translation initiation factor activity / rescue of stalled ribosome / cell junction / double-stranded RNA binding / large ribosomal subunit / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / intracellular membrane-bounded organelle / GTPase activity / GTP binding / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
![]() | Kummer E / Leibundgut M | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. Authors: Kummer E / Leibundgut M / Rackham O / Lee RG / Boehringer D / Filipovska A / Ban N | ||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
-
Downloads & links
-EMDB archive
Map data | ![]() | 15.6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 88.4 KB 88.4 KB | Display Display | ![]() |
Images | ![]() | 149.9 KB | ||
Masks | ![]() | 84.6 MB | ![]() | |
Filedesc metadata | ![]() | 17.2 KB | ||
Others | ![]() ![]() | 71.8 MB 71.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 435.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 434.7 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gb2MC ![]() 4368C ![]() 4369C ![]() 6gawC ![]() 6gazC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : mammalian mitochondrial translation initiation complex
+Supramolecule #1: mammalian mitochondrial translation initiation complex
+Supramolecule #2: mammalian mitochondrial ribosome
+Supramolecule #3: Translation initiation factor IF-2, mitochondrial
+Supramolecule #4: tRNA
+Macromolecule #1: Mitochondrial ribosomal protein L12
+Macromolecule #2: Mitochondrial ribosomal protein L27
+Macromolecule #3: Mitochondrial ribosomal protein L28
+Macromolecule #4: Mitochondrial ribosomal protein L47
+Macromolecule #5: 'Mitochondrial ribosomal protein L30
+Macromolecule #6: 'Mitochondrial ribosomal protein L55
+Macromolecule #7: Mitochondrial ribosomal protein L32
+Macromolecule #8: Mitochondrial ribosomal protein L33
+Macromolecule #9: Mitochondrial ribosomal protein L34
+Macromolecule #10: Mitochondrial ribosomal protein L35
+Macromolecule #11: Ribosomal protein
+Macromolecule #14: Translation initiation factor IF-2, mitochondrial
+Macromolecule #15: Mitochondrial ribosomal protein L2
+Macromolecule #16: ICT1
+Macromolecule #17: Mitochondrial ribosomal protein L4
+Macromolecule #18: Mitochondrial ribosomal protein L9
+Macromolecule #19: Mitochondrial ribosomal protein L10
+Macromolecule #20: Mitochondrial ribosomal protein L11
+Macromolecule #21: Mitochondrial ribosomal protein L13
+Macromolecule #22: Mitochondrial ribosomal protein L14
+Macromolecule #23: Mitochondrial ribosomal protein L15
+Macromolecule #24: Mitochondrial ribosomal protein L16
+Macromolecule #25: Mitochondrial ribosomal protein L17
+Macromolecule #26: Mitochondrial ribosomal protein L18
+Macromolecule #27: Mitochondrial ribosomal protein L19
+Macromolecule #28: Mitochondrial ribosomal protein L20
+Macromolecule #29: Mitochondrial ribosomal protein L21
+Macromolecule #30: Mitochondrial ribosomal protein L22
+Macromolecule #31: Mitochondrial ribosomal protein L23
+Macromolecule #32: Mitochondrial ribosomal protein L24
+Macromolecule #33: Mitochondrial ribosomal protein L37
+Macromolecule #34: Mitochondrial ribosomal protein L38
+Macromolecule #35: Mitochondrial ribosomal protein L39
+Macromolecule #36: Mitochondrial ribosomal protein L40
+Macromolecule #37: Mitochondrial ribosomal protein L41
+Macromolecule #38: Mitochondrial ribosomal protein L42
+Macromolecule #39: Mitochondrial ribosomal protein L43
+Macromolecule #40: Mitochondrial ribosomal protein L44
+Macromolecule #41: Mitochondrial ribosomal protein L45
+Macromolecule #42: Mitochondrial ribosomal protein L46
+Macromolecule #43: Mitochondrial ribosomal protein L48
+Macromolecule #44: Mrpl34
+Macromolecule #45: Mitochondrial ribosomal protein L50
+Macromolecule #46: Mitochondrial ribosomal protein L51
+Macromolecule #47: Mitochondrial ribosomal protein L52
+Macromolecule #48: mL53, MRPL53
+Macromolecule #49: Uncharacterized protein
+Macromolecule #50: Mitochondrial ribosomal protein L57
+Macromolecule #51: Mitochondrial ribosomal protein L58
+Macromolecule #52: 'Mitochondrial ribosomal protein L59
+Macromolecule #53: mL65, MRPS30
+Macromolecule #54: Mitochondrial ribosomal protein S18A
+Macromolecule #55: unassigned secondary structure elements
+Macromolecule #12: 16S ribosomal RNA, mitochondrial
+Macromolecule #13: CP tRNAPhe, mitochondrial
+Macromolecule #56: P-site fMet-tRNAMet, mitochondrial
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: ZINC ION
+Macromolecule #59: GUANOSINE-5'-MONOPHOSPHATE
+Macromolecule #60: SPERMINE
+Macromolecule #61: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
+Macromolecule #62: SODIUM ION
+Macromolecule #63: N-FORMYLMETHIONINE
+Macromolecule #64: water
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.171 mg/mL |
---|---|
Buffer | pH: 7.6 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
Details | contains 55S mitochondrial ribosome, mitochondrial initiation factor 2, mitochondrial formyl-Met-tRNAMet and MT-CO3 mRNA |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 13936 / Average exposure time: 1.4 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 56.9 |
---|---|
Output model | ![]() PDB-6gb2: |