[English] 日本語
![](img/lk-miru.gif)
- EMDB-34047: Cryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex w... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex with two RsmA protein dimers | |||||||||||||||
![]() | ||||||||||||||||
![]() |
| |||||||||||||||
![]() | RNA-protein complex / RNA / RNA BINDING PROTEIN-RNA complex | |||||||||||||||
Function / homology | ![]() regulation of carbohydrate metabolic process / mRNA catabolic process / positive regulation of translational initiation / negative regulation of translational initiation / mRNA 5'-UTR binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||||||||
![]() | Jia X / Pan Z / Yuan Y / Luo B / Luo Y / Mukherjee S / Jia G / Ling X / Yang X / Wu Y ...Jia X / Pan Z / Yuan Y / Luo B / Luo Y / Mukherjee S / Jia G / Ling X / Yang X / Wu Y / Liu T / Wei X / Bujnick JM / Zhao K / Su Z | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Structural basis of sRNA RsmZ regulation of Pseudomonas aeruginosa virulence. Authors: Xinyu Jia / Zhiling Pan / Yang Yuan / Bingnan Luo / Yongbo Luo / Sunandan Mukherjee / Guowen Jia / Liu Liu / Xiaobin Ling / Xiting Yang / Zhichao Miao / Xiawei Wei / Janusz M Bujnicki / ...Authors: Xinyu Jia / Zhiling Pan / Yang Yuan / Bingnan Luo / Yongbo Luo / Sunandan Mukherjee / Guowen Jia / Liu Liu / Xiaobin Ling / Xiting Yang / Zhichao Miao / Xiawei Wei / Janusz M Bujnicki / Kelei Zhao / Zhaoming Su / ![]() ![]() | |||||||||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 40.3 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 16 KB 16 KB | Display Display | ![]() |
Images | ![]() | 30.1 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() | 39.8 MB 39.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 746.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 745.7 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yr6MC ![]() 7yr7C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_34047_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_34047_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : RNP1-4
Entire | Name: RNP1-4 |
---|---|
Components |
|
-Supramolecule #1: RNP1-4
Supramolecule | Name: RNP1-4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Translational regulator CsrA
Macromolecule | Name: Translational regulator CsrA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 6.198266 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MLILTRRVGE TLMVGDDVTV TVLGVKGNQV RIGVNAPKEV AVHREEIYQR IQKEK UniProtKB: Translational regulator CsrA |
-Macromolecule #2: RsmZ RNA
Macromolecule | Name: RsmZ RNA / type: rna / ID: 2 / Number of copies: 1 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 38.400934 KDa |
Sequence | String: GCGUACAGGG AACACGCAAC CCCGAAGGAU CGGGGAAGGG ACGUCGCCAG GGAGGCGAUU CCAUCAGGAU GAUGACGAGG GACUGAAGA GUGGGCGGGG UAAUACCCCG CCCCUUUUU |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 59.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: OTHER |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 211463 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Initial model |
| ||||||
---|---|---|---|---|---|---|---|
Refinement | Space: REAL / Protocol: AB INITIO MODEL | ||||||
Output model | ![]() PDB-7yr6: |