7YR7 | pdb_00007yr7

Cryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex with three RsmA protein dimers

• PDB DOI: https://doi.org/10.2210/pdb7YR7/pdb
• EM Map EMD-34048: EMDB EMDataResource
• NAKB: 7YR7

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-08-09 Released: 2023-05-17 
• Deposition Author(s): 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 Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC), Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Structural basis of sRNA RsmZ regulation of Pseudomonas aeruginosa virulence.

Jia, X., Pan, Z., Yuan, Y., Luo, B., Luo, Y., Mukherjee, S., Jia, G., Liu, L., Ling, X., Yang, X., Miao, Z., Wei, X., Bujnicki, J.M., Zhao, K., Su, Z.

(2023) Cell Res 33: 328-330

• PubMed: 36828938 
• DOI: https://doi.org/10.1038/s41422-023-00786-3
• Primary Citation Related Structures: 
  7YR6, 7YR7

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Organizational Affiliation: 
• The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China.
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109, Warsaw, Poland.
Department of Conservative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.
Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China.
Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China. [e-mail].
The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 6-mer - A6 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis, surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 75.59 kDa 
• Atom Count: 5,102 
• Modeled Residue Count: 448 
• Deposited Residue Count: 448 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translational regulator CsrA	A [auth F], B [auth E], C [auth G], D [auth B], F [auth C], G [auth D]	55	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: csrA, PAMH27_4484
UniProt
Find proteins for O69078 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore O69078  Go to UniProtKB:  O69078

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RsmZ RNA (118-MER)	E [auth A]	118	Pseudomonas aeruginosa

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFA1301900
National Natural Science Foundation of China (NSFC)	China	32070049
National Natural Science Foundation of China (NSFC)	China	31970131
Other government		20822401D4057

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2024-07-03
  Changes: Data collection, Refinement description
• Version 1.2: 2025-03-12
  Changes: Data collection, Database references, Structure summary