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- EMDB-43173: Structure of YicC endoribonuclease bound to an RNA substrate -

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Basic information

Entry
Database: EMDB / ID: EMD-43173
TitleStructure of YicC endoribonuclease bound to an RNA substrate
Map data
Sample
  • Complex: Complex of endoribonuclease YicC bound to RNA
    • Complex: endoribonuclease YicC
      • Protein or peptide: Endoribonuclease YicC
    • Complex: RNA
      • RNA: RNA (26-MER)
  • Ligand: water
Keywordsendoribonuclease / hexamer / e. coli / HYDROLASE
Function / homology
Function and homology information


RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / cytosol
Similarity search - Function
Conserved hypothetical protein CHP00255 / YicC-like, N-terminal / Domain of unknown function DUF1732 / Endoribonuclease YicC-like, N-terminal region / Endoribonuclease YicC-like, C-terminal
Similarity search - Domain/homology
Endoribonuclease YicC
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsWu R / Lazarus MB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124838 United States
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Structural insights into RNA cleavage by a novel family of bacterial RNases.
Authors: Ruoxi Wu / Shakti Ingle / Sarah A Barnes / Heather R Dahlin / Susmita Khamrui / Yufei Xiang / Yi Shi / David H Bechhofer / Michael B Lazarus /
Abstract: Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, ...Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, we report a 2.8-Å-resolution crystal structure of the E. coli YicC apo protein and a 3.2-Å-cryo-EM structure of YicC bound to an RNA substrate. The apo YicC forms a dimer of trimers with a large open channel. In the RNA-bound form, the top trimer of YicC rotates nearly 70° and closes the RNA substrate inside the cavity to form a clamshell-pearl conformation that resembles no other known RNases. The structural information combined with mass spectrometry and biochemical data identified cleavage on the upstream side of an RNA hairpin. Mutagenesis studies demonstrated that the previously uncharacterized domain, DUF1732, is critical in both RNA binding and catalysis. These studies shed light on the mechanism of the previously unexplored YicC RNase family.
History
DepositionDec 20, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43173.png

Downloads & links

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Map

FileDownload / File: emd_43173.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.137
Minimum - Maximum-1.028158 - 1.6275226
Average (Standard dev.)0.0019428658 (±0.058046643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.00002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43173_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_43173_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of endoribonuclease YicC bound to RNA

EntireName: Complex of endoribonuclease YicC bound to RNA
Components
  • Complex: Complex of endoribonuclease YicC bound to RNA
    • Complex: endoribonuclease YicC
      • Protein or peptide: Endoribonuclease YicC
    • Complex: RNA
      • RNA: RNA (26-MER)
  • Ligand: water

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Supramolecule #1: Complex of endoribonuclease YicC bound to RNA

SupramoleculeName: Complex of endoribonuclease YicC bound to RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: endoribonuclease YicC

SupramoleculeName: endoribonuclease YicC / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Macromolecule #1: Endoribonuclease YicC

MacromoleculeName: Endoribonuclease YicC / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 33.361031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMIRSMTAY ARREIKGEWG SATWEMRSVN QRYLETYFRL PEQFRSLEPV VRERIRSRLT RGKVECTLRY EPDVSAQGEL ILNEKLAKQ LVTAANWVKM QSDEGEINPV DILRWPGVMA AQEQDLDAIA AEILAALDGT LDDFIVARET EGQALKALIE Q RLEGVTAE ...String:
GSMIRSMTAY ARREIKGEWG SATWEMRSVN QRYLETYFRL PEQFRSLEPV VRERIRSRLT RGKVECTLRY EPDVSAQGEL ILNEKLAKQ LVTAANWVKM QSDEGEINPV DILRWPGVMA AQEQDLDAIA AEILAALDGT LDDFIVARET EGQALKALIE Q RLEGVTAE VVKVRSHMPE ILQWQRERLV AKLEDAQVQL ENNRLEQELV LLAQRIDVAE ELDRLEAHVK ETYNILKKKE AV GRRLDFM MQEFNRESNT LASKSINAEV TNSAIELKVL IEQMREQIQN IE

UniProtKB: Endoribonuclease YicC

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Macromolecule #2: RNA (26-MER)

MacromoleculeName: RNA (26-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.501202 KDa
SequenceString:
GGCAGAAGAA UGCUGUAAAA CAGAGA

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration5 mg/mL
BufferpH: 7.5 / Details: 20 mM HEPES pH 7.5, 150 mM NaCl, 1 mM TCEP
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 22.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8ver

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 342211
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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