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Yorodumi- EMDB-17360: Cryo-EM structure of the anaerobic ribonucleotide reductase from ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17360 | |||||||||||||||
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Title | Cryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric state produced in the presence of dATP and CTP | |||||||||||||||
Map data | Map post-processed using DeepEMhancer | |||||||||||||||
Sample |
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Keywords | ribonucleotide reductase glycyl radical enzyme allosteric regulation nucleotide biosynthesis / OXIDOREDUCTASE / 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: 2.59 Å | |||||||||||||||
Authors | Banerjee I / Bimai O / Sjoberg BM / Logan DT | |||||||||||||||
Funding support | Sweden, United States, 4 items
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Citation | Journal: eLife / Year: 2023 Title: Activity modulation in anaerobic ribonucleotide reductase: nucleotide binding to the ATP-cone mediates long-range order-disorder transitions in the active site Authors: Bimai O / Banerjee I / Rozman Grinberg I / Huang P / Lundin D / Sjoberg BM / Logan DT | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17360.map.gz | 318 MB | EMDB map data format | |
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Header (meta data) | emd-17360-v30.xml emd-17360.xml | 24.8 KB 24.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17360_fsc.xml | 14.7 KB | Display | FSC data file |
Images | emd_17360.png | 66.5 KB | ||
Masks | emd_17360_msk_1.map | 343 MB | Mask map | |
Others | emd_17360_additional_1.map.gz emd_17360_half_map_1.map.gz emd_17360_half_map_2.map.gz | 317.5 MB 318.1 MB 318.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17360 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17360 | HTTPS FTP |
-Validation report
Summary document | emd_17360_validation.pdf.gz | 717.7 KB | Display | EMDB validaton report |
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Full document | emd_17360_full_validation.pdf.gz | 717.3 KB | Display | |
Data in XML | emd_17360_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | emd_17360_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17360 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17360 | HTTPS FTP |
-Related structure data
Related structure data | 8p2cMC 8p23C 8p2dC 8p2sC 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_17360.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Map post-processed using DeepEMhancer | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8464 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17360_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_17360_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_17360_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_17360_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 t...
Entire | Name: Anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric, dATP/CTP-bound state |
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Components |
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-Supramolecule #1: Anaerobic ribonucleotide reductase from Prevotella copri in its t...
Supramolecule | Name: Anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric, dATP/CTP-bound state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Prevotella copri (bacteria) |
Molecular weight | Theoretical: 336.8 KDa |
-Macromolecule #1: Anaerobic ribonucleoside-triphosphate reductase
Macromolecule | Name: Anaerobic ribonucleoside-triphosphate reductase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / 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: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Macromolecule | Name: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: DTP |
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Molecular weight | Theoretical: 491.182 Da |
Chemical component information | ChemComp-DTP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 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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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER | |||||||||||||||||||||
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: 11780 / Average exposure time: 2.0 sec. / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 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 | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Manual fitting was done using Coot and automatic real space refinement used phenix.refine |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: correlation coefficient |
Output model | PDB-8p2c: |