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Yorodumi- EMDB-17373: Cryo-EM structure of the anaerobic ribonucleotide reductase from ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17373 | |||||||||||||||
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Title | Cryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its dimeric, ATP/dTTP/GTP-bound state | |||||||||||||||
Map data | Locally sharpened using deepEMhancer | |||||||||||||||
Sample |
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Keywords | ribonucleotide reductase glycyl radical enzyme allosteric regulation nucleotide biosynthesis / BIOSYNTHETIC PROTEIN | |||||||||||||||
Function / homology | Ribonucleoside-triphosphate reductase, anaerobic / Anaerobic ribonucleoside-triphosphate reductase / ribonucleoside-triphosphate reductase (thioredoxin) activity / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / DNA replication / ATP binding / Anaerobic ribonucleoside-triphosphate reductase Function and homology information | |||||||||||||||
Biological species | Prevotella copri (bacteria) / Segatella copri (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||||||||
Authors | Bimai O / Banerjee I / Sjoberg BM / Logan DT | |||||||||||||||
Funding support | Sweden, United States, 4 items
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Citation | Journal: Elife / Year: 2024 Title: Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding. Authors: Ornella Bimai / Ipsita Banerjee / Inna Rozman Grinberg / Ping Huang / Lucas Hultgren / Simon Ekström / Daniel Lundin / Britt-Marie Sjöberg / Derek T Logan / Abstract: A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding adenosine triphosphate (ATP) or deoxyadenosine ...A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding adenosine triphosphate (ATP) or deoxyadenosine triphosphate (dATP) it regulates the enzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs has revealed a plethora of ways in which dATP inhibits activity by inducing oligomerisation and preventing a productive radical transfer from one subunit to the active site in the other. Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and the basis for their dATP-dependent inhibition is completely unknown. We present biochemical, biophysical, and structural information on the effects of ATP and dATP binding to the anaerobic RNR from . The enzyme exists in a dimer-tetramer equilibrium biased towards dimers when two ATP molecules are bound to the ATP-cone and tetramers when two dATP molecules are bound. In the presence of ATP, NrdD is active and has a fully ordered glycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-cone results in loss of activity and increased dynamics of the GRD, such that it cannot be detected in the cryo-EM structures. The glycyl radical is formed even in the dATP-bound form, but the substrate does not bind. The structures implicate a complex network of interactions in activity regulation that involve the GRD more than 30 Å away from the dATP molecules, the allosteric substrate specificity site and a conserved but previously unseen flap over the active site. Taken together, the results suggest that dATP inhibition in anaerobic RNRs acts by increasing the flexibility of the flap and GRD, thereby preventing both substrate binding and radical mobilisation. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17373.map.gz | 213.3 MB | EMDB map data format | |
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Header (meta data) | emd-17373-v30.xml emd-17373.xml | 24.9 KB 24.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17373_fsc.xml | 13.1 KB | Display | FSC data file |
Images | emd_17373.png | 106.1 KB | ||
Masks | emd_17373_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-17373.cif.gz | 7.1 KB | ||
Others | emd_17373_additional_1.map.gz emd_17373_half_map_1.map.gz emd_17373_half_map_2.map.gz | 123 MB 226.8 MB 226.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17373 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17373 | HTTPS FTP |
-Validation report
Summary document | emd_17373_validation.pdf.gz | 739.8 KB | Display | EMDB validaton report |
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Full document | emd_17373_full_validation.pdf.gz | 739.4 KB | Display | |
Data in XML | emd_17373_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | emd_17373_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17373 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17373 | HTTPS FTP |
-Related structure data
Related structure data | 8p2sMC 8p23C 8p27C 8p28C 8p2cC 8p2dC 8p39C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17373.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Locally sharpened using deepEMhancer | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.824 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17373_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map from non-uniform refinement in cryoSPARC
File | emd_17373_additional_1.map | ||||||||||||
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Annotation | Unsharpened map from non-uniform refinement in cryoSPARC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A from non-uniform refinement in cryoSPARC
File | emd_17373_half_map_1.map | ||||||||||||
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Annotation | Half map A from non-uniform refinement in cryoSPARC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B from non-uniform refinement in cryoSPARC
File | emd_17373_half_map_2.map | ||||||||||||
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Annotation | Half map B from non-uniform refinement in cryoSPARC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Anaerobic ribonucleotide reductase from Prevotella copri in its d...
Entire | Name: Anaerobic ribonucleotide reductase from Prevotella copri in its dimeric, ATP/dTTP/GTP-bound state |
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Components |
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-Supramolecule #1: Anaerobic ribonucleotide reductase from Prevotella copri in its d...
Supramolecule | Name: Anaerobic ribonucleotide reductase from Prevotella copri in its dimeric, ATP/dTTP/GTP-bound state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Prevotella copri (bacteria) |
Molecular weight | Theoretical: 168.4 KDa |
-Macromolecule #1: Anaerobic ribonucleoside-triphosphate reductase
Macromolecule | Name: Anaerobic ribonucleoside-triphosphate reductase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Segatella copri (bacteria) |
Molecular weight | Theoretical: 84.636055 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPGSMIQTVV KRDGRIVGFN EQKIMAAIRK AMLHTDKGED TTLIEQITDH ISYRGKSQMS VEAIQDAIEM ELMKSARKDV AQKYIAYRN QRNIARKAKT RDVFMSIVNA KNNDITRENA NMNADTPAGM MMKFASETTK PFVDDYLLSE DVRDAVMHNY I HIHDKDYY ...String: GPGSMIQTVV KRDGRIVGFN EQKIMAAIRK AMLHTDKGED TTLIEQITDH ISYRGKSQMS VEAIQDAIEM ELMKSARKDV AQKYIAYRN QRNIARKAKT RDVFMSIVNA KNNDITRENA NMNADTPAGM MMKFASETTK PFVDDYLLSE DVRDAVMHNY I HIHDKDYY PTKSLTCVQH PLDVILNHGF TAGHGSSRPA KRIETAAVLA CISLETCQNE MHGGQAIPAF DFYLAPYVRM SY QEEVKNL EKLTGEDLSN LYDAPIDDYI EKPLDGLQGR ERLEQHAINK TVNRVHQAME AFIHNMNTIH SRGGNQVVFS SIN YGTDTS AEGRCIMREI LQSTYQGVGN GETAIFPIQI WKKKRGVNYL PEDRNYDLYK LACKVTARRF FPNFLNLDAT FNQN EKWRA DDPERYKWEI ATMGCRTRVF EDRWGEKTSI ARGNLSFSTI NIVKLAIECM GIENEKQRID MFFAKLDNIL DITAK QLDE RFQFQKTAMA KQFPLLMKYL WVGAENLKPE ETIESVINHG TLGIGFIGLA ECLVALIGKH HGESEKAQEL GLKIIT YMR DRANEFSEQY HHNYSILATP AEGLSGKFTK KDRKQFGVIP GVTDRDYYTN SNHVPVYYKC TALKKAQIEA PYHDLTR GG HIFYVEIDGD ATHNPSVIES VVDMMDKYNM GYGSVNHNRN RCLDCGYENA DAHLEVCPKC GSHHIDKLQR ITGYLVGT T DRWNSGKLAE LHDRVTHIGG EK UniProtKB: Anaerobic ribonucleoside-triphosphate reductase |
-Macromolecule #2: THYMIDINE-5'-TRIPHOSPHATE
Macromolecule | Name: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: TTP |
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Molecular weight | Theoretical: 482.168 Da |
Chemical component information | ChemComp-TTP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 1, 5s blot time. |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 16667 / Average exposure time: 2.0 sec. / Average electron dose: 46.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: experimental model Details: Half of a previously-built tetrameric form of the same enzyme |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 50 |
Output model | PDB-8p2s: |