[English] 日本語
Yorodumi- EMDB-26629: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26629 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex, from focused classification and refinement (I-A) | |||||||||
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 / GTPase activity / GTP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 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
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_26629.map.gz | 255.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-26629-v30.xml emd-26629.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
Images | emd_26629.png | 193.1 KB | ||
Masks | emd_26629_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-26629.cif.gz | 6.4 KB | ||
Others | emd_26629_additional_1.map.gz emd_26629_half_map_1.map.gz emd_26629_half_map_2.map.gz | 418.7 MB 474.4 MB 474.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26629 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26629 | HTTPS FTP |
-Validation report
Summary document | emd_26629_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_26629_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_26629_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_26629_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26629 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26629 | HTTPS FTP |
-Related structure data
Related structure data | 7unqMC 7unrC 7untC 7unuC 7unvC 7unwC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
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 |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_26629.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_26629_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S...
File | emd_26629_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex (I-A). Sharpened map. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S...
File | emd_26629_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex (I-A). Half-map. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S...
File | emd_26629_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex (I-A). Half-map. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome ...
Entire | Name: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex, from focused classification and refinement (I-A) |
---|---|
Components |
|
-Supramolecule #1: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome ...
Supramolecule | Name: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex, from focused classification and refinement (I-A) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
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 |
---|---|
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 |
-Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: GDP |
---|---|
Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-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
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
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
---|---|
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-7unq: |