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- EMDB-17359: Cryo-EM structure of the anaerobic ribonucleotide reductase from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-17359
TitleCryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric, dATP-bound state
Map dataMap locally sharpened using DeepEMhancer
Sample
  • Complex: Anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric, dATP-bound state
    • Protein or peptide: Anaerobic ribonucleoside-triphosphate reductase
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsribonucleotide reductase glycyl radical enzyme allosteric regulation nucleotide biosynthesis / oxidoreductase
Function / homologyRibonucleoside-triphosphate reductase, anaerobic / Anaerobic ribonucleoside-triphosphate reductase / ribonucleoside-triphosphate reductase activity / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / DNA replication / ATP binding / Anaerobic ribonucleoside-triphosphate reductase
Function and homology information
Biological speciesPrevotella copri (bacteria) / Segatella copri (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsBanerjee I / Bimai O / Sjoberg BM / Logan DT
Funding support Sweden, United States, 4 items
OrganizationGrant numberCountry
Swedish Research Council2016-04855 Sweden
Swedish Research Council2019-01400 Sweden
CancerfondenCAN 20 1210 PjF Sweden
Wenner-Gren Foundation United States
CitationJournal: To Be Published
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
DepositionMay 15, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17359.png

Downloads & links

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Map

FileDownload / File: emd_17359.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap locally sharpened using DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 448 pix.
= 388.685 Å		0.87 Å/pix.
x 448 pix.
= 388.685 Å		0.87 Å/pix.
x 448 pix.
= 388.685 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8676 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.0017290052 - 2.2284365
Average (Standard dev.)0.00089918 (±0.022445874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 388.6848 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map from cryoSPARC with C2 symmetry

Fileemd_17359_additional_1.map
Annotationunsharpened map from cryoSPARC with C2 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17359_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17359_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Anaerobic ribonucleotide reductase from Prevotella copri in its t...

EntireName: Anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric, dATP-bound state
Components
  • Complex: Anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric, dATP-bound state
    • Protein or peptide: Anaerobic ribonucleoside-triphosphate reductase
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Anaerobic ribonucleotide reductase from Prevotella copri in its t...

SupramoleculeName: Anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric, dATP-bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Prevotella copri (bacteria)
Molecular weightTheoretical: 336.8 KDa

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Macromolecule #1: Anaerobic ribonucleoside-triphosphate reductase

MacromoleculeName: Anaerobic ribonucleoside-triphosphate reductase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Segatella copri (bacteria)
Molecular weightTheoretical: 84.636055 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: DTP
Molecular weightTheoretical: 491.182 Da
Chemical component information

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMHEPES-NaOHHEPES buffer
100.0 mMKClpotassium chloride
0.5 mMTCEPtris(2-carboxyethyl)phosphine
10.0 mMMgCl2magnesium chloride
0.5 mMdATPDeoxyadenosine triphosphatedeoxyadenosine triphosphate
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 1, 5s blot time.

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7544324
Startup modelType of model: OTHER / Details: ab initio model from cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 2 / Avg.num./class: 950000 / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Details: Non-uniform refinement in cryoSPARC / Number images used: 1349133
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
source_name: SwissModel, initial_model_type: in silico modelinitial model
source_name: AlphaFold, initial_model_type: in silico modelused to model difficult loops
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 45 / Target criteria: correlation coefficient
Output model

PDB-8p28:
Cryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric, dATP-bound state

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