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- PDB-7yr7: Cryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yr7 | |||||||||||||||
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Title | Cryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex with three RsmA protein dimers | |||||||||||||||
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![]() | RNA BINDING PROTEIN/RNA / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||
![]() | Jia, X. / Pan, Z. / Yuan, Y. / Luo, B. / Luo, Y. / Mukherjee, S. / Jia, G. / Liu, L. / Ling, X. / Yang, X. ...Jia, X. / Pan, Z. / Yuan, Y. / Luo, B. / Luo, Y. / Mukherjee, S. / Jia, G. / Liu, L. / Ling, X. / Yang, X. / Wu, Y. / Liu, T. / Miao, Z. / Wei, X. / Bujnicki, J.M. / Zhao, K. / Su, Z. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124 KB | Display | ![]() |
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PDB format | ![]() | 92.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34048MC ![]() 7yr6C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 6198.266 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: RNA chain | | Mass: 38400.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: RNP1-6 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 59.7 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 483925 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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