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- EMDB-46698: S. thermophilus class III ribonucleotide reductase with dATP and TTP -

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Basic information

Entry
Database: EMDB / ID: EMD-46698
TitleS. thermophilus class III ribonucleotide reductase with dATP and TTP
Map data
Sample
  • Complex: S. thermophilus class III ribonucleotide reductase dimer with allosteric effectors dATP and TTP
    • Protein or peptide: Anaerobic ribonucleoside-triphosphate reductase
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • 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: To Be Published
Title: Structural investigation of allosteric activity regulation in class III ribonucleotide reductases
Authors: Andree GA / Miller KR / Smith AK / Dawson CD / Deredge DJ / Drennan CL
History
DepositionAug 22, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46698.png

Downloads & links

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Map

FileDownload / File: emd_46698.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: 4.33
Minimum - Maximum0.0 - 18.296247000000001
Average (Standard dev.)0.16669871 (±0.720939)
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 dATP and TTP
Components
  • Complex: S. thermophilus class III ribonucleotide reductase dimer with allosteric effectors dATP and TTP
    • Protein or peptide: Anaerobic ribonucleoside-triphosphate reductase
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • 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 dATP 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: THYMIDINE-5'-TRIPHOSPHATE

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

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE

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Macromolecule #3: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: DTP
Molecular weightTheoretical: 491.182 Da
Chemical component information

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

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Macromolecule #4: MAGNESIUM ION

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

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / 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: 51.43 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 correctionType: 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 / Number images used: 1420860
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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