+Open data
-Basic information
Entry | Database: PDB / ID: 7p3q | ||||||||||||||||||
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Title | Streptomyces coelicolor dATP/ATP-loaded NrdR octamer | ||||||||||||||||||
Components | Transcriptional repressor NrdR | ||||||||||||||||||
Keywords | DNA BINDING PROTEIN / Repressor / Dodecamer / ATP-binding / dATP-binding | ||||||||||||||||||
Function / homology | Function and homology information negative regulation of DNA-templated transcription / DNA binding / zinc ion binding / ATP binding Similarity search - Function | ||||||||||||||||||
Biological species | Streptomyces coelicolor A3 | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å | ||||||||||||||||||
Authors | Martinez-Carranza, M. / Stenmark, P. | ||||||||||||||||||
Funding support | Sweden, 5items
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Citation | Journal: Nat Commun / Year: 2022 Title: A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases. Authors: Inna Rozman Grinberg / Markel Martínez-Carranza / Ornella Bimai / Ghada Nouaïria / Saher Shahid / Daniel Lundin / Derek T Logan / Britt-Marie Sjöberg / Pål Stenmark / Abstract: Ribonucleotide reductase (RNR) is an essential enzyme that catalyzes the synthesis of DNA building blocks in virtually all living cells. NrdR, an RNR-specific repressor, controls the transcription of ...Ribonucleotide reductase (RNR) is an essential enzyme that catalyzes the synthesis of DNA building blocks in virtually all living cells. NrdR, an RNR-specific repressor, controls the transcription of RNR genes and, often, its own, in most bacteria and some archaea. NrdR senses the concentration of nucleotides through its ATP-cone, an evolutionarily mobile domain that also regulates the enzymatic activity of many RNRs, while a Zn-ribbon domain mediates binding to NrdR boxes upstream of and overlapping the transcription start site of RNR genes. Here, we combine biochemical and cryo-EM studies of NrdR from Streptomyces coelicolor to show, at atomic resolution, how NrdR binds to DNA. The suggested mechanism involves an initial dodecamer loaded with two ATP molecules that cannot bind to DNA. When dATP concentrations increase, an octamer forms that is loaded with one molecule each of dATP and ATP per monomer. A tetramer derived from this octamer then binds to DNA and represses transcription of RNR. In many bacteria - including well-known pathogens such as Mycobacterium tuberculosis - NrdR simultaneously controls multiple RNRs and hence DNA synthesis, making it an excellent target for novel antibiotics development. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p3q.cif.gz | 218.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p3q.ent.gz | 185 KB | Display | PDB format |
PDBx/mmJSON format | 7p3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/7p3q ftp://data.pdbj.org/pub/pdb/validation_reports/p3/7p3q | HTTPS FTP |
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-Related structure data
Related structure data | 13182MC 7p37C 7p3fC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 21271.629 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69980 #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-DTP / #4: Chemical | ChemComp-ZN / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Octameric assembly of dATP/ATP-loaded NrdR / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.16 MDa / Experimental value: YES |
Source (natural) | Organism: Streptomyces coelicolor A3(2) (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 60.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8702 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 598518 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7P37 Pdb chain-ID: A / Pdb chain residue range: 1-147 |