[English] 日本語
![](img/lk-miru.gif)
- EMDB-3617: Quaternary complex between SRP, SR, and SecYEG bound to the trans... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-3617 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Quaternary complex between SRP, SR, and SecYEG bound to the translating ribosome | |||||||||
![]() | 'Quaternary structure of the SRP, SR, SecYEG, and the translating ribosome' | |||||||||
![]() |
| |||||||||
Function / homology | ![]() protein insertion into membrane from inner side / cell envelope Sec protein transport complex / signal recognition particle binding / protein transport by the Sec complex / intracellular protein transmembrane transport / signal recognition particle / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane ...protein insertion into membrane from inner side / cell envelope Sec protein transport complex / signal recognition particle binding / protein transport by the Sec complex / intracellular protein transmembrane transport / signal recognition particle / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane, translocation / protein targeting to membrane / stringent response / protein secretion / protein transmembrane transporter activity / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / protein targeting / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / intracellular protein transport / response to radiation / ribosomal large subunit assembly / cytoplasmic side of plasma membrane / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / GTPase activity / negative regulation of DNA-templated transcription / mRNA binding / GTP binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
![]() | Jomaa A / Hwang Fu Y / Boerhinger D / Leibundgut M / Shan SO / Ban N | |||||||||
![]() | ![]() Title: Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome. Authors: Ahmad Jomaa / Yu-Hsien Hwang Fu / Daniel Boehringer / Marc Leibundgut / Shu-Ou Shan / Nenad Ban / ![]() ![]() Abstract: During co-translational protein targeting, the signal recognition particle (SRP) binds to the translating ribosome displaying the signal sequence to deliver it to the SRP receptor (SR) on the ...During co-translational protein targeting, the signal recognition particle (SRP) binds to the translating ribosome displaying the signal sequence to deliver it to the SRP receptor (SR) on the membrane, where the signal peptide is transferred to the translocon. Using electron cryo-microscopy, we have determined the structure of a quaternary complex of the translating Escherichia coli ribosome, the SRP-SR in the 'activated' state and the translocon. Our structure, supported by biochemical experiments, reveals that the SRP RNA adopts a kinked and untwisted conformation to allow repositioning of the 'activated' SRP-SR complex on the ribosome. In addition, we observe the translocon positioned through interactions with the SR in the vicinity of the ribosome exit tunnel where the signal sequence is extending beyond its hydrophobic binding groove of the SRP M domain towards the translocon. Our study provides new insights into the mechanism of signal sequence transfer from the SRP to the translocon. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 116.3 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 58.6 KB 58.6 KB | Display Display | ![]() |
Images | ![]() | 171.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 300.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 299.2 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ncoMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 'Quaternary structure of the SRP, SR, SecYEG, and the translating ribosome' | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : Ribosome nascent chain, SRP, SR, and SecYEG quaternary complex
+Supramolecule #1: Ribosome nascent chain, SRP, SR, and SecYEG quaternary complex
+Supramolecule #2: Ribosome
+Supramolecule #3: SRP, SR, and SecYEG
+Macromolecule #1: 4.5S SRP RNA (Ffs)
+Macromolecule #2: P-site tRNA-CCA end
+Macromolecule #3: 23S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #5: 50S ribosomal protein L2
+Macromolecule #6: 50S ribosomal protein L3
+Macromolecule #7: 50S ribosomal protein L4
+Macromolecule #8: 50S ribosomal protein L5
+Macromolecule #9: 50S ribosomal protein L6
+Macromolecule #10: 50S ribosomal protein L9
+Macromolecule #11: 50S ribosomal protein L10
+Macromolecule #12: 50S ribosomal protein L11
+Macromolecule #13: 50S ribosomal protein L13
+Macromolecule #14: 50S ribosomal protein L14
+Macromolecule #15: 50S ribosomal protein L15
+Macromolecule #16: 50S ribosomal protein L16
+Macromolecule #17: 50S ribosomal protein L17
+Macromolecule #18: 50S ribosomal protein L18
+Macromolecule #19: 50S ribosomal protein L19
+Macromolecule #20: 50S ribosomal protein L20
+Macromolecule #21: 50S ribosomal protein L21
+Macromolecule #22: 50S ribosomal protein L22
+Macromolecule #23: 50S ribosomal protein L23
+Macromolecule #24: 50S ribosomal protein L24
+Macromolecule #25: 50S ribosomal protein L25
+Macromolecule #26: 50S ribosomal protein L27
+Macromolecule #27: 50S ribosomal protein L28
+Macromolecule #28: 50S ribosomal protein L29
+Macromolecule #29: 50S ribosomal protein L30
+Macromolecule #30: 50S ribosomal protein L32
+Macromolecule #31: 50S ribosomal protein L33
+Macromolecule #32: 50S ribosomal protein L34
+Macromolecule #33: 50S ribosomal protein L35
+Macromolecule #34: 50S ribosomal protein L36
+Macromolecule #35: Protein translocase subunit SecY
+Macromolecule #36: Protein translocase subunit SecE
+Macromolecule #37: Signal recognition particle protein,Signal recognition particle p...
+Macromolecule #38: Protein-export membrane protein SecG
+Macromolecule #39: Signal sequence (1A9L)
+Macromolecule #40: Signal recognition particle receptor FtsY
+Macromolecule #41: ZINC ION
+Macromolecule #42: TETRAFLUOROALUMINATE ION
+Macromolecule #43: MAGNESIUM ION
+Macromolecule #44: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.1 mg/mL |
---|---|
Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Min: 78.0 K / Max: 85.0 K |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: OTHER / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 100719 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |
---|---|
Output model | ![]() PDB-5nco: |