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- EMDB-62856: CryoEM structure of class Ib RNR from Mycobacterium thermoresisti... -

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Basic information

Entry
Database: EMDB / ID: EMD-62856
TitleCryoEM structure of class Ib RNR from Mycobacterium thermoresistibile, conformer G
Map data
Sample
  • Complex: Ternary complex of RNR
    • Complex: Heterotetrameric asymmetric complex of RNR
      • Other: Ribonucleotide reductase alpha subunit
      • Protein or peptide: Ribonucleotide reductase beta subunit
    • Other: Ribonucleotide reductase NrdI subunit
KeywordsEnzyme complex / supply Dexoyribonucleotides for replication and repair / asymmetric complex / REPLICATION
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.53 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_62856.png

Downloads & links

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Map

FileDownload / File: emd_62856.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: 0.1
Minimum - Maximum-0.34531155 - 0.92323977
Average (Standard dev.)0.00029573977 (±0.03133883)
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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Mask #1

Fileemd_62856_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: hide dust at size 8

Fileemd_62856_half_map_1.map
Annotationhide dust at size 8
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: hide dust at size 8

Fileemd_62856_half_map_2.map
Annotationhide dust at size 8
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of RNR

EntireName: Ternary complex of RNR
Components
  • Complex: Ternary complex of RNR
    • Complex: Heterotetrameric asymmetric complex of RNR
      • Other: Ribonucleotide reductase alpha subunit
      • Protein or peptide: Ribonucleotide reductase beta subunit
    • Other: Ribonucleotide reductase NrdI subunit

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Supramolecule #1: Ternary complex of RNR

SupramoleculeName: Ternary complex of RNR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)

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Supramolecule #2: Heterotetrameric asymmetric complex of RNR

SupramoleculeName: Heterotetrameric asymmetric complex of RNR / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
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 RIEDNMESIG ...String:
MLNLYDADGK IQFDKDKQAA REFFLQHVNQ NTVFFHDYDE KLDYLIENDY YEPEVLDQYS RDFVKSLLDR AYAKKFRFPT FLGAFKYYTS YTLKTFDGKR YLERFEDRVV MVALTLAAGD VELAEKLVDE IMDGRFQPAT PTFLNSGKKQ RGEPVSCFLL RIEDNMESIG RAINSALQLS KRGGGVALLL SNVREFGAPI KNIENQSSGV IPIMKLLEDS FSYANQLGAR QGAGAVYLHA HHPDIYRFLD TKRENADEKI RIKTLSLGVV IPDITFELAK KNEDMYLFSP YDVERVYGVP FADISVTEKY YEMVDNPRIR KSKINAREFF QTLAELQFES GYPYIMFEDT VNRSNPIEGK VTHSNLCSEI LQVSTPSEFN DDLSYKVVGK DISCNLGSLN IAKAMDSPDF GQTVEVAIRA LTAVSDQTRI DSVPSIVRGN DESHSIGLGQ MNLHGYLGRE RIFYGSEEAI DFTNMYFYTV CYHAVRASNR IAIERGKHFV GFEKSKYATG EFFDKYTDQV WEPKTDKVRE LFAKANIHIP TQEDWRRLKE SVQKHGIYNA YLQAVPPTGS ISYINHSTSS IHPIASKIEI RKEGKIGRVY YPAPYMTNDN LEYFQDAYEI GYEKIIDTYA AATQHVDQGL SLTLFFKDTA TTRDVNKAQI YAWRKGIKTL YYIRLRQMAL EGTEVEGCVS CML
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #3: Ribonucleotide reductase NrdI subunit

MacromoleculeName: Ribonucleotide reductase NrdI subunit / type: other / ID: 3 / Classification: other
Source (natural)Organism: Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
SequenceString: V T V G G L V Y F S S V S E Y T H R F V E K L G L P A T R I P L H G R I E V D E P Y V L I L P T Y G G G R A T P D I N H G G Y V P K Q V I A F L N N E H N R S L L R G V I A A ...String:
V T V G G L V Y F S S V S E Y T H R F V E K L G L P A T R I P L H G R I E V D E P Y V L I L P T Y G G G R A T P D I N H G G Y V P K Q V I A F L N N E H N R S L L R G V I A A G N T N F G A E F A Y A G N V V S R K C G V P Y L Y R F E L M G T P D D V E A V R A G L A D F W K E Q T C H L P S Q L Q S R

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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 FLFYSGFYLP ...String:
MKLVNRVSAI NWNRLEDDKD AEVWHRLTGN FWLPEKVPVS NDIPSWNTLT DTEKQLTMRV FTGLTLLDTI QGTVGAVSLI PDALTPHEEA VLTNIAFMES VHAKSYSNIF STLCSTAEID DAFRWSEENP NLQRKAEIVM QYYRGDEPLK RKVASTLLES FLFYSGFYLP MYWSSRAKLT NTADMIRLII RDEAVHGYYI GYKYQRGLAM VEPAKQKELK DYTDLLFELY DNEVEYTQDL YDDVGLTEDV KKFLRYNANK ALMNLGYEAL FPKDETDVNP AILSALAPNA DENHDFFSGS GSSYVIGKAV VTEDEDWDF

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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 MaCl, 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: 1.05 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: 4.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.2) / Number images used: 16462
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 modelPDB ID:

2bq1


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: dimer of NrdE chain used
RefinementSpace: REAL

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