+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23972 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Mtb 70SIC in complex with MtbEttA at Trans_R1 state | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | mycobacterium tuberculosis / ABCF ribosome complex / antibiotic / RIBOSOME | |||||||||
Function / homology | Function and homology information negative regulation of translational elongation / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / peptidoglycan-based cell wall / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome binding / regulation of translation / ribosomal small subunit assembly / 5S rRNA binding ...negative regulation of translational elongation / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / peptidoglycan-based cell wall / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome binding / regulation of translation / ribosomal small subunit assembly / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) / Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Cui Z / Zhang J | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23972.map.gz | 92.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-23972-v30.xml emd-23972.xml | 73.9 KB 73.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23972_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_23972.png | 113.2 KB | ||
Filedesc metadata | emd-23972.cif.gz | 14.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23972 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23972 | HTTPS FTP |
-Validation report
Summary document | emd_23972_validation.pdf.gz | 602.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_23972_full_validation.pdf.gz | 602 KB | Display | |
Data in XML | emd_23972_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_23972_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23972 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23972 | HTTPS FTP |
-Related structure data
Related structure data | 7mszMC 7mscC 7mshC 7msmC 7mt2C 7mt3C 7mt7C 7mu0C C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_23972.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : The complex of Mtb 70SIC with MtbEttA at ATP-hydrolysis transitio...
+Supramolecule #1: The complex of Mtb 70SIC with MtbEttA at ATP-hydrolysis transitio...
+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 #53: Energy-dependent translational throttle protein EttA
+Macromolecule #9: 23S rRNA
+Macromolecule #10: 5S rRNA
+Macromolecule #34: 16S rRNA
+Macromolecule #54: initiator tRNA (Met)
+Macromolecule #55: mRNA
+Macromolecule #56: ZINC ION
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #59: VANADATE ION
+Macromolecule #60: N-FORMYLMETHIONINE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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 |