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- PDB-7yr6: Cryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex w... -

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Basic information

Entry
Database: PDB / ID: 7yr6
TitleCryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex with two RsmA protein dimers
Components
  • RsmZ RNA
  • Translational regulator CsrA
KeywordsRNA BINDING PROTEIN/RNA / RNA-protein complex / RNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


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
Translational regulator CsrA / Carbon storage regulator superfamily / Global regulator protein family
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Translational regulator CsrA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsJia, 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, J.M. / Zhao, K. / Su, Z.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
National Natural Science Foundation of China (NSFC)32070049 China
National Natural Science Foundation of China (NSFC)31970131 China
Other government20822041D4057
CitationJournal: Cell Res / Year: 2023
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
DepositionAug 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Translational regulator CsrA
D: Translational regulator CsrA
C: Translational regulator CsrA
B: Translational regulator CsrA
A: RsmZ RNA


Theoretical massNumber of molelcules
Total (without water)63,1945
Polymers63,1945
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Translational regulator CsrA / Carbon storage regulator


Mass: 6198.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: csrA, PAMH27_4484 / Production host: Escherichia coli (E. coli) / References: UniProt: V6AK05
#2: RNA chain RsmZ RNA


Mass: 38400.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RNP1-4 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1700 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 59.7 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameCategory
7UCSF Chimeramodel fitting
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 211463 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeSource nameType
12MF0

2mf0

12MF0PDBexperimental model
24KJI

4kji

14KJIPDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034541
ELECTRON MICROSCOPYf_angle_d0.8166722
ELECTRON MICROSCOPYf_dihedral_angle_d18.0452459
ELECTRON MICROSCOPYf_chiral_restr0.044871
ELECTRON MICROSCOPYf_plane_restr0.004412

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