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- EMDB-46693: S. thermophilus class III ribonucleotide reductase focused refine... -

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Basic information

Entry
Database: EMDB / ID: EMD-46693
TitleS. thermophilus class III ribonucleotide reductase focused refined core
Map data
Sample
  • Complex: S. thermophilus class III ribonucleotide reductase dimer with allosteric effectors dATP and TTP
KeywordsRibonucleotide reductase / allosteric regulation / cone domain / glycyl radical enzyme / OXIDOREDUCTASE
Biological speciesStreptococcus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsAndree GA / Drennan CL
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126982 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)T32ES007020 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Sci Adv / Year: 2025
Title: How ATP and dATP reposition class III ribonucleotide reductase cone domains to regulate enzyme activity.
Authors: Gisele A Andree / Kelsey R Miller-Brown / Zhuangyu Zhao / Ally K Smith / Christopher D Dawson / Daniel J Deredge / Catherine L Drennan /
Abstract: Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides. In the majority of cases, RNR activity is allosterically regulated by the cellular 2'- ...Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides. In the majority of cases, RNR activity is allosterically regulated by the cellular 2'-deoxyadenosine 5'-triphosphate (dATP)/adenosine 5'-triphosphate (ATP) ratio. To investigate allosteric activity regulation in anaerobic or class III (glycyl radical containing) RNRs, we determine cryo-electron microscopy structures of the class III RNR from (StNrdD). We find that StNrdD's regulatory "cone" domains adopt markedly different conformations depending on whether the activator ATP or the inhibitor dATP is bound and that these different conformations alternatively position an "active site flap" toward the active site (ATP-bound) or away (dATP-bound). In contrast, the position of the glycyl radical domain is unaffected by the cone domain conformations, suggesting that StNrdD activity is regulated through control of substrate binding rather than control of radical transfer. Hydrogen-deuterium exchange mass spectrometry and mutagenesis support the structural findings. In addition, our structural data provide insight into the molecular basis by which ATP and dATP binding lead to the observed differential cone domain conformations.
History
DepositionAug 22, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46693.png

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Map

FileDownload / File: emd_46693.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00549
Minimum - Maximum-0.007439469 - 0.02881638
Average (Standard dev.)0.00002146138 (±0.0009143654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.992 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_46693_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_46693_half_map_2.map
Projections & Slices
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Sample components

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Entire : S. thermophilus class III ribonucleotide reductase dimer with all...

EntireName: S. thermophilus class III ribonucleotide reductase dimer with allosteric effectors dATP and TTP
Components
  • Complex: S. thermophilus class III ribonucleotide reductase dimer with allosteric effectors dATP and TTP

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Supramolecule #1: S. thermophilus class III ribonucleotide reductase dimer with all...

SupramoleculeName: S. thermophilus class III ribonucleotide reductase dimer with allosteric effectors dATP and TTP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptococcus thermophilus (bacteria)

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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

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.43 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 4.0.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 942509
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.0)

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