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Open data
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Basic information
| Entry | Database: EMDB / ID: EMD-23975 | |||||||||
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| Title | Mtb 70S with P/E tRNA | |||||||||
 Map data | ||||||||||
 Sample | 
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 Keywords | Mycobacterium tuberculosis / ribosome / ABCF ribosome complex / Antibiotic | |||||||||
| Function / homology |  Function and homology informationpeptidoglycan-based cell wall / large ribosomal subunit / regulation of translation / 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 ...peptidoglycan-based cell wall / large ribosomal subunit / regulation of translation / 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 / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function  | |||||||||
| Biological species |  Mycobacterium tuberculosis H37Rv (bacteria) /  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) / ![]() ![]()  | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
 Authors | Cui Z / Zhang J | |||||||||
| Funding support |   United States, 2 items 
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 Citation |  Journal: Nat Commun / Year: 2022Title: Interplay between an ATP-binding cassette F protein and the ribosome from Mycobacterium tuberculosis. Authors: Zhicheng Cui / Xiaojun Li / Joonyoung Shin / Howard Gamper / Ya-Ming Hou / James C Sacchettini / Junjie Zhang / ![]() Abstract: EttA, energy-dependent translational throttle A, is a ribosomal factor that gates ribosome entry into the translation elongation cycle. A detailed understanding of its mechanism of action is limited ...EttA, energy-dependent translational throttle A, is a ribosomal factor that gates ribosome entry into the translation elongation cycle. A detailed understanding of its mechanism of action is limited due to the lack of high-resolution structures along its ATPase cycle. Here we present the cryo-electron microscopy (cryo-EM) structures of EttA from Mycobacterium tuberculosis (Mtb), referred to as MtbEttA, in complex with the Mtb 70S ribosome initiation complex (70SIC) at the pre-hydrolysis (ADPNP) and transition (ADP-VO) states, and the crystal structure of MtbEttA alone in the post-hydrolysis (ADP) state. We observe that MtbEttA binds the E-site of the Mtb 70SIC, remodeling the P-site tRNA and the ribosomal intersubunit bridge B7a during the ribosomal ratcheting. In return, the rotation of the 30S causes conformational changes in MtbEttA, forcing the two nucleotide-binding sites (NBSs) to alternate to engage each ADPNP in the pre-hydrolysis states, followed by complete engagements of both ADP-VO molecules in the ATP-hydrolysis transition states. In the post-hydrolysis state, the conserved ATP-hydrolysis motifs of MtbEttA dissociate from both ADP molecules, leaving two nucleotide-binding domains (NBDs) in an open conformation. These structures reveal a dynamic interplay between MtbEttA and the Mtb ribosome, providing insights into the mechanism of translational regulation by EttA-like proteins.  | |||||||||
| History | 
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Structure visualization
| Movie | 
 
 
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| Structure viewer | EM map:  SurfView Molmil Jmol/JSmol | 
| Supplemental images | 
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Downloads & links
-EMDB archive
| Map data |  emd_23975.map.gz | 93.6 MB |  EMDB map data format | |
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| Header (meta data) |  emd-23975-v30.xml emd-23975.xml | 70.5 KB 70.5 KB  | Display Display  |  EMDB header | 
| FSC (resolution estimation) |  emd_23975_fsc.xml | 11.3 KB | Display |  FSC data file | 
| Images |  emd_23975.png | 112.8 KB | ||
| Filedesc metadata |  emd-23975.cif.gz | 13.7 KB | ||
| Archive directory |  http://ftp.pdbj.org/pub/emdb/structures/EMD-23975 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23975 | HTTPS FTP  | 
-Validation report
| Summary document |  emd_23975_validation.pdf.gz | 589.6 KB | Display |  EMDB validaton report | 
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| Full document |  emd_23975_full_validation.pdf.gz | 589.1 KB | Display | |
| Data in XML |  emd_23975_validation.xml.gz | 12.2 KB | Display | |
| Data in CIF |  emd_23975_validation.cif.gz | 16.2 KB | Display | |
| Arichive directory |  https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23975 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23975 | HTTPS FTP  | 
-Related structure data
| Related structure data | ![]() 7mt3MC ![]() 7mscC ![]() 7mshC ![]() 7msmC ![]() 7mszC ![]() 7mt2C ![]() 7mt7C ![]() 7mu0C C: citing same article ( M: atomic model generated by this map  | 
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| Similar structure data | 
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Links
| EMDB pages |  EMDB (EBI/PDBe) /  EMDataResource | 
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| Related items in Molecule of the Month | 
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Map
| File |  Download / File: emd_23975.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
 
 Images are generated by Spider.  | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Density | 
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Details | EMDB XML: 
 CCP4 map header: 
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-Supplemental data
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Sample components
+Entire : Mtb 70S with P/E tRNA
+Supramolecule #1: Mtb 70S with P/E tRNA
+Macromolecule #1: 50S ribosomal protein L32
+Macromolecule #2: 50S ribosomal protein L33 2
+Macromolecule #3: 50S ribosomal protein L34
+Macromolecule #4: 50S ribosomal protein L35
+Macromolecule #5: 50S ribosomal protein L36
+Macromolecule #6: 50S ribosomal protein L31
+Macromolecule #7: 50S ribosomal protein L37
+Macromolecule #8: 50S ribosomal protein L1
+Macromolecule #11: 50S ribosomal protein L2
+Macromolecule #12: 50S ribosomal protein L3
+Macromolecule #13: 50S ribosomal protein L4
+Macromolecule #14: 50S ribosomal protein L5
+Macromolecule #15: 50S ribosomal protein L6
+Macromolecule #16: 50S ribosomal protein L9
+Macromolecule #17: 50S ribosomal protein L13
+Macromolecule #18: 50S ribosomal protein L14
+Macromolecule #19: 50S ribosomal protein L15
+Macromolecule #20: 50S ribosomal protein L16
+Macromolecule #21: 50S ribosomal protein L17
+Macromolecule #22: 50S ribosomal protein L18
+Macromolecule #23: 50S ribosomal protein L19
+Macromolecule #24: 50S ribosomal protein L20
+Macromolecule #25: 50S ribosomal protein L21
+Macromolecule #26: 50S ribosomal protein L22
+Macromolecule #27: 50S ribosomal protein L23
+Macromolecule #28: 50S ribosomal protein L24
+Macromolecule #29: 50S ribosomal protein L25
+Macromolecule #30: 50S ribosomal protein L27
+Macromolecule #31: 50S ribosomal protein L28
+Macromolecule #32: 50S ribosomal protein L29
+Macromolecule #33: 50S ribosomal protein L30
+Macromolecule #35: 30S ribosomal protein S3
+Macromolecule #36: 30S ribosomal protein S4
+Macromolecule #37: 30S ribosomal protein S5
+Macromolecule #38: 30S ribosomal protein S6
+Macromolecule #39: 30S ribosomal protein S7
+Macromolecule #40: 30S ribosomal protein S8
+Macromolecule #41: 30S ribosomal protein S9
+Macromolecule #42: 30S ribosomal protein S10
+Macromolecule #43: 30S ribosomal protein S11
+Macromolecule #44: 30S ribosomal protein S12
+Macromolecule #45: 30S ribosomal protein S13
+Macromolecule #46: 30S ribosomal protein S14 type Z
+Macromolecule #47: 30S ribosomal protein S15
+Macromolecule #48: 30S ribosomal protein S16
+Macromolecule #49: 30S ribosomal protein S17
+Macromolecule #50: 30S ribosomal protein S18 1
+Macromolecule #51: 30S ribosomal protein S19
+Macromolecule #52: 30S ribosomal protein S20
+Macromolecule #9: 23S rRNA
+Macromolecule #10: 5S rRNA
+Macromolecule #34: 16S rRNA
+Macromolecule #53: tRNA (Met)
+Macromolecule #54: mRNA
+Macromolecule #55: ZINC ION
+Macromolecule #56: MAGNESIUM ION
-Experimental details
-Structure determination
| Method | cryo EM | 
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 Processing | single particle reconstruction | 
| Aggregation state | particle | 
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Sample preparation
| Buffer | pH: 7.5 | 
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| Grid | Model: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 | 
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K | 
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Electron microscopy
| Microscope | FEI TITAN KRIOS | 
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| Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 48.0 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 | 
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company  | 
Movie
Controller
About Yorodumi



Keywords
Mycobacterium tuberculosis H37Rv (bacteria)
Authors
United States, 2 items 
Citation
UCSF Chimera































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





















Processing


