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Yorodumi- EMDB-26553: N2 sub-domain of IF2 bound to the 30S subunit in the Pseudomonas ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26553 | |||||||||
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Title | N2 sub-domain of IF2 bound to the 30S subunit in the Pseudomonas aeruginosa 70S ribosome initiation complex (focused classification and refinement) | |||||||||
Map data | N2 sub-domain of IF2 bound to the 30S subunit in the 70S ribosome initiation complex. Focused map. | |||||||||
Sample |
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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 / GTPase activity / GTP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Basu RS / Sherman MB / Gagnon MG | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation. Authors: Ritwika S Basu / Michael B Sherman / Matthieu G Gagnon / Abstract: During translation initiation, initiation factor 2 (IF2) holds initiator transfer RNA (fMet-tRNA) in a specific orientation in the peptidyl (P) site of the ribosome. Upon subunit joining IF2 ...During translation initiation, initiation factor 2 (IF2) holds initiator transfer RNA (fMet-tRNA) in a specific orientation in the peptidyl (P) site of the ribosome. Upon subunit joining IF2 hydrolyzes GTP and, concomitant with inorganic phosphate (P) release, changes conformation facilitating fMet-tRNA accommodation into the P site and transition of the 70 S ribosome initiation complex (70S-IC) to an elongation-competent ribosome. The mechanism by which IF2 separates from initiator tRNA at the end of translation initiation remains elusive. Here, we report cryo-electron microscopy (cryo-EM) structures of the 70S-IC from Pseudomonas aeruginosa bound to compact IF2-GDP and initiator tRNA. Relative to GTP-bound IF2, rotation of the switch 2 α-helix in the G-domain bound to GDP unlocks a cascade of large-domain movements in IF2 that propagate to the distal tRNA-binding domain C2. The C2-domain relocates 35 angstroms away from tRNA, explaining how IF2 makes way for fMet-tRNA accommodation into the P site. Our findings provide the basis by which IF2 gates the ribosome to the elongation phase. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26553.map.gz | 256.2 MB | EMDB map data format | |
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Header (meta data) | emd-26553-v30.xml emd-26553.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
Images | emd_26553.png | 215.3 KB | ||
Masks | emd_26553_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-26553.cif.gz | 6.1 KB | ||
Others | emd_26553_additional_1.map.gz emd_26553_half_map_1.map.gz emd_26553_half_map_2.map.gz | 388.6 MB 475.4 MB 475.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26553 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26553 | HTTPS FTP |
-Validation report
Summary document | emd_26553_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_26553_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_26553_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_26553_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26553 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26553 | HTTPS FTP |
-Related structure data
Related structure data | 7uiuMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&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
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26553.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | N2 sub-domain of IF2 bound to the 30S subunit in the 70S ribosome initiation complex. Focused map. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26553_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: N2 sub-domain of IF2 bound to the 30S...
File | emd_26553_additional_1.map | ||||||||||||
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Annotation | N2 sub-domain of IF2 bound to the 30S subunit in the 70S ribosome initiation complex. Sharpened focused map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: N2 sub-domain of IF2 bound to the 30S...
File | emd_26553_half_map_1.map | ||||||||||||
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Annotation | N2 sub-domain of IF2 bound to the 30S subunit in the 70S ribosome initiation complex. Half-map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: N2 sub-domain of IF2 bound to the 30S...
File | emd_26553_half_map_2.map | ||||||||||||
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Annotation | N2 sub-domain of IF2 bound to the 30S subunit in the 70S ribosome initiation complex. Half-map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Focused map of the N2 sub-domain of IF2 bound to the 30S subunit ...
Entire | Name: Focused map of the N2 sub-domain of IF2 bound to the 30S subunit in the 70S ribosome initiation complex |
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Components |
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-Supramolecule #1: Focused map of the N2 sub-domain of IF2 bound to the 30S subunit ...
Supramolecule | Name: Focused map of the N2 sub-domain of IF2 bound to the 30S subunit in the 70S ribosome initiation complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Pseudomonas aeruginosa PAO1 (bacteria) |
-Macromolecule #1: Translation initiation factor IF-2
Macromolecule | Name: Translation initiation factor IF-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa PAO1 (bacteria) |
Molecular weight | Theoretical: 91.049641 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTQVTVKELA QVVDTPVERL LLQMRDAGLP HTSAEQVVTD SEKQALLTHL KGSHGDRASE PRKITLQRKT TTTLKVGGSK TVSVEVRKK KTYVKRSPDE IEAERQRELE EQRAAEEAER LKAEEAAARQ RAEEEARKAE EAARAKAAQE AAATAGAEPA V VADVAVAE ...String: MTQVTVKELA QVVDTPVERL LLQMRDAGLP HTSAEQVVTD SEKQALLTHL KGSHGDRASE PRKITLQRKT TTTLKVGGSK TVSVEVRKK KTYVKRSPDE IEAERQRELE EQRAAEEAER LKAEEAAARQ RAEEEARKAE EAARAKAAQE AAATAGAEPA V VADVAVAE PVAKPAAVEE RKKEEPRRVP KRDEDDDRRD RKHTQHRPSV KEKEKVPAPR VAPRSTDEES DGYRRGGRGG KS KLKKRNQ HGFQNPTGPI VREVNIGETI TVAELAAQMS VKGAEVVKFM FKMGSPVTIN QVLDQETAQL VAEELGHKVK LVS ENALEE QLAESLKFEG EAVTRAPVVT VMGHVDHGKT SLLDYIRRAK VAAGEAGGIT QHIGAYHVET ERGMVTFLDT PGHA AFTAM RARGAQATDI VILVVAADDG VMPQTQEAVQ HAKAAGVPIV VAVNKIDKPE ANPDNIKNGL AALDVIPEEW GGDAP FVPV SAKLGTGVDE LLEAVLLQAE VLELKATPSA PGRGVVVESR LDKGRGPVAT VLVQDGTLRQ GDMVLVGINY GRVRAM LDE NGKPIKEAGP SIPVEILGLD GTPDAGDEMT VVADEKKARE VALFRQGKFR EVKLARAHAG KLENIFENMG QEEKKTL NI VLKADVRGSL EALQGSLSGL GNDEVQVRVV GGGVGGITES DANLALASNA VLFGFNVRAD AGARKIVEAE GLDMRYYN V IYDIIEDVKK ALTGMLGSDL RENILGIAEV RDVFRSPKFG AIAGCMVTEG MVHRNRPIRV LRDDVVIFEG ELESLRRFK DDVAEVRAGM ECGIGVKSYN DVKVGDKIEV FEKVEVARSL UniProtKB: Translation initiation factor IF-2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | TFS KRIOS |
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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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7uiu: |