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- EMDB-46747: S. thermophilus class III ribonucleotide reductase with ATP and TTP -

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Basic information

Entry
Database: EMDB / ID: EMD-46747
TitleS. thermophilus class III ribonucleotide reductase with ATP and TTP
Map data
Sample
  • Complex: S. thermophilus class III ribonucleotide reductase dimer with allosteric effectors ATP and TTP
    • Protein or peptide: Anaerobic ribonucleoside-triphosphate reductase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: water
KeywordsRibonucleotide reductase / allosteric regulation / cone domain / glycyl radical enzyme / OXIDOREDUCTASE
Function / homology
Function and homology information


ribonucleoside-triphosphate reductase (thioredoxin) / anaerobic ribonucleoside-triphosphate reductase complex / ribonucleoside-triphosphate reductase (thioredoxin) activity / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / DNA replication / ATP binding
Similarity search - Function
Ribonucleoside-triphosphate reductase, anaerobic / Anaerobic ribonucleoside-triphosphate reductase / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Glycine radical domain / Glycine radical domain profile. / ATP-cone domain / ATP cone domain / ATP-cone domain profile.
Similarity search - Domain/homology
Anaerobic ribonucleoside-triphosphate reductase
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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 25, 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_46747.png

Downloads & links

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Map

FileDownload / File: emd_46747.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.33
Minimum - Maximum0.0 - 16.442806000000001
Average (Standard dev.)0.14981844 (±0.6662399)
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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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 ATP and TTP
Components
  • Complex: S. thermophilus class III ribonucleotide reductase dimer with allosteric effectors ATP and TTP
    • Protein or peptide: Anaerobic ribonucleoside-triphosphate reductase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: water

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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 ATP and TTP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptococcus thermophilus (bacteria)

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Macromolecule #1: Anaerobic ribonucleoside-triphosphate reductase

MacromoleculeName: Anaerobic ribonucleoside-triphosphate reductase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: ribonucleoside-triphosphate reductase (thioredoxin)
Source (natural)Organism: Streptococcus thermophilus (bacteria)
Molecular weightTheoretical: 83.563508 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIILEKERVT VNPDIKVIKR DGRMVTFDSS KIYEAILKAS ETITPITPLI ETKLEGIANR VVAEINDRFS HNIKIYEIQS IVEHELLEA NEYAIAQEYI NYRTKRDFER SQATDINFTI NKLVNKDQAV VHENANKDSD LYNTQRDLTA GIVGKSVGLK M LPPHVANA ...String:
MIILEKERVT VNPDIKVIKR DGRMVTFDSS KIYEAILKAS ETITPITPLI ETKLEGIANR VVAEINDRFS HNIKIYEIQS IVEHELLEA NEYAIAQEYI NYRTKRDFER SQATDINFTI NKLVNKDQAV VHENANKDSD LYNTQRDLTA GIVGKSVGLK M LPPHVANA HQKGDIHFHD LDYSPYTPMT NCCLIDFKGM LANGFKIGNA EVESPKSIQT ATAQISQIIA NVASSQYGGC TA DRIDEFL APYAELNYKK HLADAKEWVT EEKQEDYARA KTRKDIYDAM QSLEYEINTL FTSNGQTPFT SLGFGLGTNW FER EIQKAI LQVRILGLGS EHRTAIFPKL IFTLKRGLNL EPNSPNYDIK QLALECATKR MYPDVLSYDK IIELTGSFKA PMGC RSFLQ GWKDENGVEV NSGRMNLGVV TLNLPRIALE SKGDQDKFWE IFEERMGIAK DALVYRVERV KEATPANAPI LYQYG AFGQ RLRKCDSVDQ LFKHRRATVS LGYIGLYEVA SVFYGSDWET NLEAKTFTLN IVKAMKNACE SWSDEYDYHF SVYSTP SES LTDRFCRLDT EKFGVVTDIT DKEYYTNSFH YDVRKNPTPF EKLEFEKDYP EAGATGGFIH YCEYPVLQQN PKALEAV WD FAYDRVGYLG TNTPIDKCYK CDFEGDFTPT ERGFMCPNCG NTDPKTVDVV KRTCGYLGNP QARPMVKGRH KEISARVK H MNGSTIKYGG KHL

UniProtKB: Anaerobic ribonucleoside-triphosphate reductase

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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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Macromolecule #4: THYMIDINE-5'-TRIPHOSPHATE

MacromoleculeName: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: TTP
Molecular weightTheoretical: 482.168 Da
Chemical component information

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 51.35 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 290300
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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