[English] 日本語
 Yorodumi
Yorodumi- EMDB-26635: Pseudomonas aeruginosa 70S ribosome initiation complex bound to I... -
+ Open data
Open data
- Basic information
Basic information
| Entry |  | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Title | Pseudomonas aeruginosa 70S ribosome initiation complex bound to IF2-GDPCP (structure II-B) | |||||||||
|  Map data | ||||||||||
|  Sample | 
 | |||||||||
|  Keywords | Initiation Factor 2 / 70S ribosome / cryo-EM / translation initiation / initiator tRNA / conformational changes / RIBOSOME | |||||||||
| Function / homology |  Function and homology information translation initiation factor activity / translational initiation / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit ...translation initiation factor activity / translational initiation / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / RNA binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
| Biological species |  Pseudomonas aeruginosa PAO1 (bacteria) /   Escherichia coli (E. coli) /  Bacteriophage sp. (virus) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
|  Authors | Basu RS / Sherman MB / Gagnon MG | |||||||||
| Funding support |  United States, 2 items 
 | |||||||||
|  Citation |  Journal: Nat Commun / Year: 2022 Title: Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation Authors: Basu RS / Sherman MB / Gagnon MG | |||||||||
| History | 
 | 
- Structure visualization
Structure visualization
| Supplemental images | 
|---|
- Downloads & links
Downloads & links
-EMDB archive
| Map data |  emd_26635.map.gz | 256.7 MB |  EMDB map data format | |
|---|---|---|---|---|
| Header (meta data) |  emd-26635-v30.xml  emd-26635.xml | 89.3 KB 89.3 KB | Display Display |  EMDB header | 
| Images |  emd_26635.png | 248.5 KB | ||
| Masks |  emd_26635_msk_1.map | 512 MB |  Mask map | |
| Filedesc metadata |  emd-26635.cif.gz | 16.7 KB | ||
| Others |  emd_26635_additional_1.map.gz  emd_26635_half_map_1.map.gz  emd_26635_half_map_2.map.gz | 384.8 MB 475.9 MB 475.9 MB | ||
| Archive directory |  http://ftp.pdbj.org/pub/emdb/structures/EMD-26635  ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26635 | HTTPS FTP | 
-Validation report
| Summary document |  emd_26635_validation.pdf.gz | 1.1 MB | Display |  EMDB validaton report | 
|---|---|---|---|---|
| Full document |  emd_26635_full_validation.pdf.gz | 1.1 MB | Display | |
| Data in XML |  emd_26635_validation.xml.gz | 19.1 KB | Display | |
| Data in CIF |  emd_26635_validation.cif.gz | 22.7 KB | Display | |
| Arichive directory |  https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26635  ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26635 | HTTPS FTP | 
-Related structure data
| Related structure data |  7unwMC  7unqC  7unrC  7untC  7unuC  7unvC M: atomic model generated by this map C: citing same article ( | 
|---|---|
| Similar structure data | Similarity search - Function & homology  F&H Search | 
| EM raw data |  EMPIAR-11012 (Title: Pseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2 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]) | 
- Links
Links
| EMDB pages |  EMDB (EBI/PDBe) /  EMDataResource | 
|---|---|
| Related items in Molecule of the Month | 
- Map
Map
| File |  Download / File: emd_26635.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & slices | Image control
 
 Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
| Density | 
 | ||||||||||||||||||||||||||||||||||||
| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML: 
 | 
-Supplemental data
-Mask #1
| File |  emd_26635_msk_1.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | 
 | ||||||||||||
| Density Histograms | 
-Additional map: Pseudomonas aeruginosa 70S ribosome initiation complex bound to...
| File | emd_26635_additional_1.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Pseudomonas aeruginosa 70S ribosome initiation complex bound to IF2-GDPCP (structure II-B). Sharpened map. | ||||||||||||
| Projections & Slices | 
 | ||||||||||||
| Density Histograms | 
-Half map: Pseudomonas aeruginosa 70S ribosome initiation complex bound to...
| File | emd_26635_half_map_1.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Pseudomonas aeruginosa 70S ribosome initiation complex bound to IF2-GDPCP (structure II-B). Half-map. | ||||||||||||
| Projections & Slices | 
 | ||||||||||||
| Density Histograms | 
-Half map: Pseudomonas aeruginosa 70S ribosome initiation complex bound to...
| File | emd_26635_half_map_2.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Pseudomonas aeruginosa 70S ribosome initiation complex bound to IF2-GDPCP (structure II-B). Half-map. | ||||||||||||
| Projections & Slices | 
 | ||||||||||||
| Density Histograms | 
- Sample components
Sample components
+Entire : Pseudomonas aeruginosa 70S ribosome initiation complex bound to I...
+Supramolecule #1: Pseudomonas aeruginosa 70S ribosome initiation complex bound to I...
+Macromolecule #1: 16S Ribosomal RNA
+Macromolecule #22: P-site initiator tRNA
+Macromolecule #23: mRNA
+Macromolecule #25: 23S Ribosomal RNA
+Macromolecule #26: 5S Ribosomal RNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein S21
+Macromolecule #24: Translation initiation factor IF-2
+Macromolecule #27: 50S ribosomal protein L2
+Macromolecule #28: 50S ribosomal protein L3
+Macromolecule #29: 50S ribosomal protein L4
+Macromolecule #30: 50S ribosomal protein L5
+Macromolecule #31: 50S ribosomal protein L6
+Macromolecule #32: 50S ribosomal protein L9
+Macromolecule #33: 50S ribosomal protein L10
+Macromolecule #34: 50S ribosomal protein L11
+Macromolecule #35: 50S ribosomal protein L13
+Macromolecule #36: 50S ribosomal protein L14
+Macromolecule #37: 50S ribosomal protein L15
+Macromolecule #38: 50S ribosomal protein L16
+Macromolecule #39: 50S ribosomal protein L17
+Macromolecule #40: 50S ribosomal protein L18
+Macromolecule #41: 50S ribosomal protein L19
+Macromolecule #42: 50S ribosomal protein L20
+Macromolecule #43: 50S ribosomal protein L21
+Macromolecule #44: 50S ribosomal protein L22
+Macromolecule #45: 50S ribosomal protein L23
+Macromolecule #46: 50S ribosomal protein L24
+Macromolecule #47: 50S ribosomal protein L25
+Macromolecule #48: 50S ribosomal protein L27
+Macromolecule #49: 50S ribosomal protein L28
+Macromolecule #50: 50S ribosomal protein L29
+Macromolecule #51: 50S ribosomal protein L30
+Macromolecule #52: 50S ribosomal protein L31
+Macromolecule #53: 50S ribosomal protein L32
+Macromolecule #54: 50S ribosomal protein L33
+Macromolecule #55: 50S ribosomal protein L34
+Macromolecule #56: 50S ribosomal protein L35
+Macromolecule #57: 50S ribosomal protein L36
+Macromolecule #58: MAGNESIUM ION
+Macromolecule #59: N-FORMYLMETHIONINE
+Macromolecule #60: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
+Macromolecule #61: ZINC ION
+Macromolecule #62: water
-Experimental details
-Structure determination
| Method | cryo EM | 
|---|---|
|  Processing | single particle reconstruction | 
| Aggregation state | particle | 
- Sample preparation
Sample preparation
| Buffer | pH: 7.6 | 
|---|---|
| Grid | Model: Quantifoil R2/1 / Pretreatment - Type: GLOW DISCHARGE | 
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295 K / Instrument: LEICA EM GP | 
- Electron microscopy
Electron microscopy
| Microscope | TFS KRIOS | 
|---|---|
| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8056 / Average exposure time: 1.0 sec. / Average electron dose: 31.0 e/Å2 | 
| Electron beam | Acceleration voltage: 300 kV / Electron source:  FIELD EMISSION GUN | 
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 105000 | 
| Sample stage | Cooling holder cryogen: NITROGEN | 
| Experimental equipment |  Model: Titan Krios / Image courtesy: FEI Company | 
+ Image processing
Image processing
-Atomic model buiding 1
| Initial model | 
 | ||||||
|---|---|---|---|---|---|---|---|
| Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||
| Output model |  PDB-7unw:  | 
 Movie
Movie Controller
Controller





















 Z (Sec.)
Z (Sec.) Y (Row.)
Y (Row.) X (Col.)
X (Col.)

























































