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- EMDB-34048: Cryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-34048
TitleCryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex with three RsmA protein dimers
Map data
Sample
  • Complex: RNP1-6
    • Protein or peptide: Translational regulator CsrA
    • RNA: RsmZ RNA (118-MER)
KeywordsRNA-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
Translational regulator CsrA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsJia 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 JM / Zhao K / Su Z
Funding support China, 4 items
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 government20822401D4057
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, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34048.png

Downloads & links

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Map

FileDownload / File: emd_34048.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 224 pix.
= 190.4 Å		0.85 Å/pix.
x 224 pix.
= 190.4 Å		0.85 Å/pix.
x 224 pix.
= 190.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.205
Minimum - Maximum-1.7810152 - 2.6697931
Average (Standard dev.)0.0038689347 (±0.054128096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 190.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34048_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34048_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNP1-6

EntireName: RNP1-6
Components
  • Complex: RNP1-6
    • Protein or peptide: Translational regulator CsrA
    • RNA: RsmZ RNA (118-MER)

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Supramolecule #1: RNP1-6

SupramoleculeName: RNP1-6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: Translational regulator CsrA

MacromoleculeName: Translational regulator CsrA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 6.198266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLILTRRVGE TLMVGDDVTV TVLGVKGNQV RIGVNAPKEV AVHREEIYQR IQKEK

UniProtKB: Translational regulator CsrA

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Macromolecule #2: RsmZ RNA (118-MER)

MacromoleculeName: RsmZ RNA (118-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 38.400934 KDa
SequenceString:
GCGUACAGGG AACACGCAAC CCCGAAGGAU CGGGGAAGGG ACGUCGCCAG GGAGGCGAUU CCAUCAGGAU GAUGACGAGG GACUGAAGA GUGGGCGGGG UAAUACCCCG CCCCUUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 59.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 483925
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChain

2mf0

source_name: PDB, initial_model_type: experimental model

4kji

source_name: PDB, initial_model_type: experimental model

1vpz

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-7yr7:
Cryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex with three RsmA protein dimers

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