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- EMDB-63859: Structure of alpha subunit of class Ib Ribonucleotide reductase i... -

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Basic information

Entry
Database: EMDB / ID: EMD-63859
TitleStructure of alpha subunit of class Ib Ribonucleotide reductase in Mycobacteria (apo form)
Map data
Sample
  • Complex: Dimer of alpha subunit of RNR
    • Protein or peptide: Ribonucleoside-diphosphate reductase
KeywordsEnzyme complex / supply Dexoyribonucleotides for replication and repair / asymmetric complex / REPLICATION
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / ATP binding
Similarity search - Function
Ribonucleotide reductase N-terminal / Ribonucleotide reductase, class 1b, subunit NrdE / Ribonucleotide reductase N-terminal / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsYadav LR / Mande SC / Vinothkumar KR / Kumar J
Funding support India, 2 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)Centre of Excellence Grant (BT/PR15450/COE/34/46/2016) India
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: To Be Published
Title: Structural basis of half-site reactivity in Class Ib ribonucleotide reductases
Authors: Yadav LR / Mande SC
History
DepositionMar 20, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63859.png

Downloads & links

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Map

FileDownload / File: emd_63859.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 288 pix.
= 302.976 Å		1.05 Å/pix.
x 288 pix.
= 302.976 Å		1.05 Å/pix.
x 288 pix.
= 302.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.0017863922 - 2.203885
Average (Standard dev.)0.0007337276 (±0.01995877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 302.976 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_63859_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63859_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_63859_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 : Dimer of alpha subunit of RNR

EntireName: Dimer of alpha subunit of RNR
Components
  • Complex: Dimer of alpha subunit of RNR
    • Protein or peptide: Ribonucleoside-diphosphate reductase

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Supramolecule #1: Dimer of alpha subunit of RNR

SupramoleculeName: Dimer of alpha subunit of RNR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)

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Macromolecule #1: Ribonucleoside-diphosphate reductase

MacromoleculeName: Ribonucleoside-diphosphate reductase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonucleoside-diphosphate reductase
Source (natural)Organism: Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Molecular weightTheoretical: 79.427633 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLNLYDADGK IQFDKDKQAA REFFLQHVNQ NTVFFHDYDE KLDYLIENDY YEPEVLDQYS RDFVKSLLDR AYAKKFRFPT FLGAFKYYT SYTLKTFDGK RYLERFEDRV VMVALTLAAG DVELAEKLVD EIMDGRFQPA TPTFLNSGKK QRGEPVSCFL L RIEDNMES ...String:
MLNLYDADGK IQFDKDKQAA REFFLQHVNQ NTVFFHDYDE KLDYLIENDY YEPEVLDQYS RDFVKSLLDR AYAKKFRFPT FLGAFKYYT SYTLKTFDGK RYLERFEDRV VMVALTLAAG DVELAEKLVD EIMDGRFQPA TPTFLNSGKK QRGEPVSCFL L RIEDNMES IGRAINSALQ LSKRGGGVAL LLSNVREFGA PIKNIENQSS GVIPIMKLLE DSFSYANQLG ARQGAGAVYL HA HHPDIYR FLDTKRENAD EKIRIKTLSL GVVIPDITFE LAKKNEDMYL FSPYDVERVY GVPFADISVT EKYYEMVDNP RIR KSKINA REFFQTLAEL QFESGYPYIM FEDTVNRSNP IEGKVTHSNL CSEILQVSTP SEFNDDLSYK VVGKDISCNL GSLN IAKAM DSPDFGQTVE VAIRALTAVS DQTRIDSVPS IVRGNDESHS IGLGQMNLHG YLGRERIFYG SEEAIDFTNM YFYTV CYHA VRASNRIAIE RGKHFVGFEK SKYATGEFFD KYTDQVWEPK TDKVRELFAK ANIHIPTQED WRRLKESVQK HGIYNA YLQ AVPPTGSISY INHSTSSIHP IASKIEIRKE GKIGRVYYPA PYMTNDNLEY FQDAYEIGYE KIIDTYAAAT QHVDQGL SL TLFFKDTATT RDVNKAQIYA WRKGIKTLYY IRLRQMALEG TEVEGCVSCM L

UniProtKB: Ribonucleoside-diphosphate reductase

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMTris
150.0 mMSodium ChlorideNaCl
1.0 mMManganase ChlorideMncl2

Details: 25mM Tris pH8, 150mM NaCl, 1mM Mncl2
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Details: 25mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER / Energy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 6935 / Average exposure time: 5.0 sec. / Average electron dose: 42.02 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 27597922
CTF correctionSoftware - Name: cryoSPARC (ver. v3.3.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.2) / Number images used: 125957
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. v3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v3.3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: alfold3 model used
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: CC
Output model

PDB-9u4z:
Structure of alpha subunit of class Ib Ribonucleotide reductase in Mycobacteria (apo form)

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