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- PDB-8p23: Cryo-EM structure of the anaerobic ribonucleotide reductase from ... -

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Basic information

Entry
Database: PDB / ID: 8p23
TitleCryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its dimeric, ATP/CTP-bound state
ComponentsAnaerobic ribonucleoside-triphosphate reductase
KeywordsBIOSYNTHETIC PROTEIN / ribonucleotide reductase glycyl radical enzyme allosteric regulation nucleotide biosynthesis
Function / homology
Function and homology information


ribonucleoside-triphosphate reductase (thioredoxin) activity / DNA replication / ATP binding
Similarity search - Function
Ribonucleoside-triphosphate reductase, anaerobic / Anaerobic ribonucleoside-triphosphate reductase / ATP-cone domain / ATP cone domain / ATP-cone domain profile.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / Anaerobic ribonucleoside-triphosphate reductase
Similarity search - Component
Biological speciesPrevotella copri (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsBanerjee, I. / Bimai, O. / Sjoberg, B.M. / Logan, D.T.
Funding support Sweden, United States, 4items
OrganizationGrant numberCountry
Swedish Research Council2016-04855 Sweden
Swedish Research Council2019-01400 Sweden
CancerfondenCAN 20 1210 PjF Sweden
Wenner-Gren Foundation United States
CitationJournal: 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, B.M. / Logan, D.T.
History
DepositionMay 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anaerobic ribonucleoside-triphosphate reductase
B: Anaerobic ribonucleoside-triphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,8498
Polymers169,2722
Non-polymers2,5776
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Anaerobic ribonucleoside-triphosphate reductase


Mass: 84636.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prevotella copri (bacteria) / Gene: BN510_01369 / Production host: Escherichia coli (E. coli) / References: UniProt: R6BY16
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Anaerobic ribonucleotide reductase from Prevotella copri in its dimeric, ATP/CTP-bound state
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.1684 MDa / Experimental value: NO
Source (natural)Organism: Prevotella copri (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPES bufferHEPES-NaOH1
2100 mMpotassium chlorideKCl1
30.5 mMtris(2-carboxyethyl)phosphineTCEP1
410 mMmagnesium chlorideMgCl21
50.5 mMdeoxyadenosine triphosphateATP1
60.5 mMcytosine triphosphateCTP1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot force 1, 5s blot time

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.1 sec. / Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17033
EM imaging opticsEnergyfilter name: GIF Bioquantum
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.2.0particle selection
2EPU2.8.1image acquisition
4cryoSPARC3.2.0CTF correction
7Coot0.9.8.7model fitting
9PHENIX1.19.2-4158model refinement
10cryoSPARC3.3.2initial Euler assignment
11cryoSPARC4.1.2final Euler assignment
12cryoSPARC3.3.2classification
13cryoSPARC3D reconstruction
CTF correctionDetails: Patch CTF correction in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 14132328
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 291231 / Num. of class averages: 8 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation coefficient
Details: Manual fitting was done using Coot and automatic real space refinement used phenix.refine
Atomic model buildingDetails: Half of a previously-built tetrameric form of the same enzyme
Source name: Other / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211623
ELECTRON MICROSCOPYf_angle_d0.50215711
ELECTRON MICROSCOPYf_dihedral_angle_d10.8344317
ELECTRON MICROSCOPYf_chiral_restr0.0461706
ELECTRON MICROSCOPYf_plane_restr0.0042013

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