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Yorodumi- PDB-8b0i: CryoEM structure of bacterial RapZ.GlmZ complex central to the co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b0i | ||||||
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Title | CryoEM structure of bacterial RapZ.GlmZ complex central to the control of cell envelope biogenesis | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / endonuclease RNase E / adaptor protein RapZ / small regulatory RNA GlmZ | ||||||
Function / homology | Function and homology information RNA destabilization / carbohydrate derivative binding / protein homotetramerization / molecular adaptor activity / GTP binding / protein-containing complex / RNA binding / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.28 Å | ||||||
Authors | Islam, M.S. / Hardwick, H.W. / Chirgadze, D.Y. / Luisi, B.F. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: EMBO J / Year: 2023 Title: Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis. Authors: Md Saiful Islam / Steven W Hardwick / Laura Quell / Svetlana Durica-Mitic / Dimitri Y Chirgadze / Boris Görke / Ben F Luisi / Abstract: Biogenesis of the essential precursor of the bacterial cell envelope, glucosamine-6-phosphate (GlcN6P), is controlled by intricate post-transcriptional networks mediated by GlmZ, a small regulatory ...Biogenesis of the essential precursor of the bacterial cell envelope, glucosamine-6-phosphate (GlcN6P), is controlled by intricate post-transcriptional networks mediated by GlmZ, a small regulatory RNA (sRNA). GlmZ stimulates translation of the mRNA encoding GlcN6P synthtase in Escherichia coli, but when bound by RapZ protein, the sRNA becomes inactivated through cleavage by the endoribonuclease RNase E. Here, we report the cryoEM structure of the RapZ:GlmZ complex, revealing a complementary match of the RapZ tetrameric quaternary structure to structural repeats in the sRNA. The nucleic acid is contacted by RapZ mostly through a highly conserved domain that shares an evolutionary relationship with phosphofructokinase and suggests links between metabolism and riboregulation. We also present the structure of a precleavage intermediate formed between the binary RapZ:GlmZ complex and RNase E that reveals how GlmZ is presented and recognised by the enzyme. The structures provide a framework for understanding how other encounter complexes might guide recognition and action of endoribonucleases on target transcripts, and how structured substrates in polycistronic precursors may be recognised for processing by RNase E. #1: Journal: Biorxiv / Year: 2022 Title: Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis Authors: Islam, M.S. / Hardwick, S.W. / Quell, L. / Chirgadze, D.Y. / Gorke, B. / Luisi, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b0i.cif.gz | 376.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b0i.ent.gz | 309.5 KB | Display | PDB format |
PDBx/mmJSON format | 8b0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b0i_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8b0i_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8b0i_validation.xml.gz | 44.7 KB | Display | |
Data in CIF | 8b0i_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/8b0i ftp://data.pdbj.org/pub/pdb/validation_reports/b0/8b0i | HTTPS FTP |
-Related structure data
Related structure data | 15784MC 8b0jC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 32538.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rapZ, yhbJ, b3205, JW3172 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A894 #2: RNA chain | | Mass: 66061.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli (E. coli) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RapZ tetramer, GlmZ stem loops I & II / Type: COMPLEX / Details: In vitro reconstituted RapZ and GlmZ complex / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 / Details: 25 mM HEPES pH 7.5, 300 KCl, and 1 mM MgCl2 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 300 nm / Nominal defocus min: 100 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 47.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||
Particle selection | Num. of particles selected: 286172 | ||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||
3D reconstruction | Resolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27551 / Symmetry type: POINT |