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- PDB-6aui: Human ribonucleotide reductase large subunit (alpha) with dATP and CDP -
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Open data
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Basic information
Entry | Database: PDB / ID: 6aui | ||||||||||||
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Title | Human ribonucleotide reductase large subunit (alpha) with dATP and CDP | ||||||||||||
![]() | Ribonucleoside-diphosphate reductase large subunit | ||||||||||||
![]() | OXIDOREDUCTASE / Ribonucleotide Reductase Electron transfer Radical chemistry Thiyl radical | ||||||||||||
Function / homology | ![]() ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / ribonucleoside diphosphate metabolic process / positive regulation of G0 to G1 transition / 2'-deoxyribonucleotide biosynthetic process / mitochondrial DNA replication / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor ...ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / ribonucleoside diphosphate metabolic process / positive regulation of G0 to G1 transition / 2'-deoxyribonucleotide biosynthetic process / mitochondrial DNA replication / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / Interconversion of nucleotide di- and triphosphates / deoxyribonucleotide biosynthetic process / protein heterotetramerization / response to ionizing radiation / DNA synthesis involved in DNA repair / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / cell projection / male gonad development / disordered domain specific binding / retina development in camera-type eye / nuclear envelope / DNA repair / neuronal cell body / mitochondrion / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
![]() | Brignole, E.J. / Drennan, C.L. / Asturias, F.J. / Tsai, K.L. / Penczek, P.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: 3.3-Å resolution cryo-EM structure of human ribonucleotide reductase with substrate and allosteric regulators bound. Authors: Edward J Brignole / Kuang-Lei Tsai / Johnathan Chittuluru / Haoran Li / Yimon Aye / Pawel A Penczek / JoAnne Stubbe / Catherine L Drennan / Francisco Asturias / ![]() Abstract: Ribonucleotide reductases (RNRs) convert ribonucleotides into deoxyribonucleotides, a reaction essential for DNA replication and repair. Human RNR requires two subunits for activity, the α subunit ...Ribonucleotide reductases (RNRs) convert ribonucleotides into deoxyribonucleotides, a reaction essential for DNA replication and repair. Human RNR requires two subunits for activity, the α subunit contains the active site, and the β subunit houses the radical cofactor. Here, we present a 3.3-Å resolution structure by cryo-electron microscopy (EM) of a dATP-inhibited state of human RNR. This structure, which was determined in the presence of substrate CDP and allosteric regulators ATP and dATP, has three α units arranged in an α ring. At near-atomic resolution, these data provide insight into the molecular basis for CDP recognition by allosteric specificity effectors dATP/ATP. Additionally, we present lower-resolution EM structures of human α in the presence of both the anticancer drug clofarabine triphosphate and β. Together, these structures support a model for RNR inhibition in which β is excluded from binding in a radical transfer competent position when α exists as a stable hexamer. | ||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 782.7 KB | Display | ![]() |
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PDB format | ![]() | 651.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 114.4 KB | Display | |
Data in CIF | ![]() | 171.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7006MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 92350.391 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): Gene inserted between NdeI and NotI sites Production host: ![]() ![]() References: UniProt: P23921, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-DTP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CDP / #5: Water | ChemComp-HOH / | |
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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 |
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Sample preparation
Component | Name: Human ribonucleotide reductase large subnunit (alpha) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Units: MEGADALTONS / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7.6 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: 14 microM alpha and 0.05 mM dATP, 3 mM ATP, 1 mM CDP in 50 mM HEPES, pH 7.6, 15 mM MgCl2, 1 mM EDTA, 5 mM DTT, and 50 mM KCl | |||||||||||||||||||||||||
Specimen support | Details: glow discharged at 20 mA in an EMITech K100X Grid was first cleaned in a Solarus 950 (Gatan) at 25 W for 10 s in 75/25 Ar/O2 gas mixture Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Protochips C-Flat | |||||||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 75 % / Chamber temperature: 277 K Details: manual blot with a strip of Whatman paper until drop stops wicking determined visually |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 7.6 sec. / Electron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2144 |
Image scans | Movie frames/image: 38 / Used frames/image: 5-38 |
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Processing
Software | Name: PHENIX / Version: dev_2650: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Symmetry | Point symmetry: D3 (2x3 fold dihedral) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43885 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||
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