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Open data
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Basic information
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Title | Streptomyces coelicolor ATP-loaded NrdR | ||||||||||||||||||
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Function / homology | Ribonucleotide reductase regulator NrdR-like / ATP-cone domain / ![]() ![]() ![]() ![]() | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() | ||||||||||||||||||
![]() | Martinez-Carranza M / Stenmark P | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 96.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.5 KB 17.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.4 KB | Display | ![]() |
Images | ![]() | 99.2 KB | ||
Others | ![]() ![]() | 95.1 MB 95.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p37MC ![]() 7p3fC ![]() 7p3qC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.67 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_13178_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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-Half map: Half map B
File | emd_13178_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Sample components
-Entire : Homododecameric assembly of ATP-loaded NrdR.
Entire | Name: Homododecameric assembly of ATP-loaded NrdR. |
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Components |
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-Supramolecule #1: Homododecameric assembly of ATP-loaded NrdR.
Supramolecule | Name: Homododecameric assembly of ATP-loaded NrdR. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
Molecular weight | Experimental: 247 KDa |
-Macromolecule #1: Transcriptional repressor NrdR
Macromolecule | Name: Transcriptional repressor NrdR / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21.271629 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MHCPFCRHPD SRVVDSRTTD DGTSIRRRRQ CPDCSRRFTT VETCSLMVVK RSGVTEPFSR TKVINGVRKA CQGRPVTEDA LAQLGQRVE EAVRATGSAE LTTHDVGLAI LGPLQELDLV AYLRFASVYR AFDSLEDFEA AIAELRETTG HPGEEDDTGA G SQENDRGP ...String: MHCPFCRHPD SRVVDSRTTD DGTSIRRRRQ CPDCSRRFTT VETCSLMVVK RSGVTEPFSR TKVINGVRKA CQGRPVTEDA LAQLGQRVE EAVRATGSAE LTTHDVGLAI LGPLQELDLV AYLRFASVYR AFDSLEDFEA AIAELRETTG HPGEEDDTGA G SQENDRGP TGAGQVPEPA GAADKLAAAL EHHHHHH |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 24 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 12 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 6317 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-7p37: |