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- EMDB-62858: CryoEM structure of classIbRibonucleotide reductase from Mycobact... -

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Basic information

Entry
Database: EMDB / ID: EMD-62858
TitleCryoEM structure of classIbRibonucleotide reductase from Mycobacterium thermoresistibile, conformer B
Map dataunsharpened map
Sample
  • Complex: Binary complex of RNR
    • Other: Ribonucleotide reductase alpha subunit
    • Protein or peptide: Ribonucleotide reductase beta subunit
KeywordsEnzyme complex / supply Dexoyribonucleotides for replication and repair / asymmetric complex / REPLICATION
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.15 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: Dynamics of Class Ib ribonucleotide reductase complex revealed by CryoEM
Authors: Yadav LR / Mande SC / Vinothkumar KR / Kumar J
History
DepositionDec 24, 2024-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62858.png

Downloads & links

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Map

FileDownload / File: emd_62858.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 288 pix.
= 306.72 Å		1.07 Å/pix.
x 288 pix.
= 306.72 Å		1.07 Å/pix.
x 288 pix.
= 306.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.26755446 - 0.6385186
Average (Standard dev.)0.000287278 (±0.027332611)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 306.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62858_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_62858_msk_2.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_62858_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_62858_half_map_2.map
Projections & Slices
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Sample components

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Entire : Binary complex of RNR

EntireName: Binary complex of RNR
Components
  • Complex: Binary complex of RNR
    • Other: Ribonucleotide reductase alpha subunit
    • Protein or peptide: Ribonucleotide reductase beta subunit

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Supramolecule #1: Binary complex of RNR

SupramoleculeName: Binary complex of RNR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Heterotetrameric asymmetric complex of RNR
Source (natural)Organism: Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)

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Macromolecule #1: Ribonucleotide reductase alpha subunit

MacromoleculeName: Ribonucleotide reductase alpha subunit / type: other / ID: 1 / Classification: other
Source (natural)Organism: Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
SequenceString: MLNLYDADGK IQFDKDKQAA REFFLQHVNQ NTVFFHDYDE KLDYLIENDY YEPEVLDQYS RDFVKSLLDR AYAKKFRFPT FLGAFKYYTS YTLKTFDGKR YLERFEDRVV MVALTLAAGD VELAEKLVDE IMDGRFQPAT PTFLNSGKKQ RGEPVSCFLL RIEDNMESI ...String:
MLNLYDADGK IQFDKDKQAA REFFLQHVNQ NTVFFHDYDE KLDYLIENDY YEPEVLDQYS RDFVKSLLDR AYAKKFRFPT FLGAFKYYTS YTLKTFDGKR YLERFEDRVV MVALTLAAGD VELAEKLVDE IMDGRFQPAT PTFLNSGKKQ RGEPVSCFLL RIEDNMESI GRAINSALQL SKRGGGVALL LSNVREFGAP IKNIENQSSG VIPIMKLLED SFSYANQLGA RQGAGAVYLH AHHPDIYRFL DTKRENADEK IRIKTLSLGV VIPDITFELA KKNEDMYLFS PYDVERVYGV PFADISVTEK YYEMVDNPRI R KSKINARE FFQTLAELQF ESGYPYIMFE DTVNRSNPIE GKVTHSNLCS EILQVSTPSE FNDDLSYKVV GKDISCNLGS LNIAKAMDSP DFGQTVEVAI RALTAVSDQT RIDSVPSIVR GNDESHSIGL GQMNLHGYLG RERIFYGSEE AIDFTNMYFY TV CYHAVRA SNRIAIERGK HFVGFEKSKY ATGEFFDKYT DQVWEPKTDK VRELFAKANI HIPTQEDWRR LKESVQKHGI YNAYLQAVPP TGSISYINHS TSSIHPIASK IEIRKEGKIG RVYYPAPYMT NDNLEYFQDA YEIGYEKIID TYAAATQHVD QGL SLTLFF KDTATTRDVN KAQIYAWRKG IKTLYYIRLR QMALEGTEVE GCVSCML
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: Ribonucleotide reductase beta subunit

MacromoleculeName: Ribonucleotide reductase beta subunit / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLVNRVSAI NWNRLEDDKD AEVWHRLTGN FWLPEKVPVS NDIPSWNTLT DTEKQLTMRV FTGLTLLDTI QGTVGAVSLI PDALTPHEEA VLTNIAFMES VHAKSYSNIF STLCSTAEID DAFRWSEENP NLQRKAEIVM QYYRGDEPLK RKVASTLLES FLFYSGFYL ...String:
MKLVNRVSAI NWNRLEDDKD AEVWHRLTGN FWLPEKVPVS NDIPSWNTLT DTEKQLTMRV FTGLTLLDTI QGTVGAVSLI PDALTPHEEA VLTNIAFMES VHAKSYSNIF STLCSTAEID DAFRWSEENP NLQRKAEIVM QYYRGDEPLK RKVASTLLES FLFYSGFYL PMYWSSRAKL TNTADMIRLI IRDEAVHGYY IGYKYQRGLA MVEPAKQKEL KDYTYDLLFE LYDNEVEYTQ DLYDDVGLTE DVKKFLRYNA NKALMNLGYE ALFPKDETDV NPAILSALAP NADENHDFFS GSGSSYVIGK AVVTEDEDWD F

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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

Concentration1.25 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMTris
150.0 mMSodium ChlorideNaCl

Details: 25mM Tris pH8, 150mM NaCl
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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV
Detailssampled crosslinked with glutaraldehyde

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 831 / Average exposure time: 8.0 sec. / Average electron dose: 47.36 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 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: 300000
CTF correctionSoftware - Name: cryoSPARC (ver. v3.3.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.2) / Number images used: 14633
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

RefinementSpace: REAL

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