[English] 日本語
Yorodumi
- EMDB-9272: EM structure of Bacillus subtilis ribonucleotide reductase inhibi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9272
TitleEM structure of Bacillus subtilis ribonucleotide reductase inhibited filament composed of NrdE alpha subunit and NrdF beta subunit with dATP
Map dataASU of Bacillus subtilis ribonucleotide reductase inhibited filament composed of NrdE alpha and NrdF beta subunits with dATP. Handedness already corrected by reference to NrdE crystal structures.
Sample
  • Complex: Inhibited filament of ribonucleoside-diphosphate reductase composed of NrdE alpha subunits and NrdF beta subunit tails
    • Protein or peptide: Ribonucleoside-diphosphate reductaseRibonucleotide reductase
    • Protein or peptide: Ribonucleoside-diphosphate reductase NrdF beta subunit
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Keywordsribonucleotide reductase / allostery / nucleotide metabolism / filament / dATP / ATP / OXIDOREDUCTASE
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / 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 / Ribonucleoside-diphosphate reductase subunit alpha
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.65 Å
AuthorsThomas WC / Bacik JP / Kaelber JT / Ando N
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124847 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100008 United States
CitationJournal: Nat Commun / Year: 2019
Title: Convergent allostery in ribonucleotide reductase.
Authors: William C Thomas / F Phil Brooks / Audrey A Burnim / John-Paul Bacik / JoAnne Stubbe / Jason T Kaelber / James Z Chen / Nozomi Ando /
Abstract: Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for ...Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a distinct and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible active tetramer and two inhibited helical filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery.
History
DepositionOct 29, 2018-
Header (metadata) releaseNov 21, 2018-
Map releaseJun 19, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6mw3
  • Surface level: 1.14
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6mw3
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9272.png

Downloads & links

-
Map

FileDownload / File: emd_9272.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationASU of Bacillus subtilis ribonucleotide reductase inhibited filament composed of NrdE alpha and NrdF beta subunits with dATP. Handedness already corrected by reference to NrdE crystal structures.
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 1.14 / Movie #1: 1.14
Minimum - Maximum-2.6790166 - 4.963113
Average (Standard dev.)0.068803266 (±0.25537685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-2.6794.9630.069

-
Supplemental data

-
Mask #1

Fileemd_9272_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered, unmasked, half-map from refinement of NrdEF

Fileemd_9272_half_map_1.map
AnnotationUnfiltered, unmasked, half-map from refinement of NrdEF
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered, unmasked half-map from refinement of NrdEF

Fileemd_9272_half_map_2.map
AnnotationUnfiltered, unmasked half-map from refinement of NrdEF
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Inhibited filament of ribonucleoside-diphosphate reductase compos...

EntireName: Inhibited filament of ribonucleoside-diphosphate reductase composed of NrdE alpha subunits and NrdF beta subunit tails
Components
  • Complex: Inhibited filament of ribonucleoside-diphosphate reductase composed of NrdE alpha subunits and NrdF beta subunit tails
    • Protein or peptide: Ribonucleoside-diphosphate reductaseRibonucleotide reductase
    • Protein or peptide: Ribonucleoside-diphosphate reductase NrdF beta subunit
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

-
Supramolecule #1: Inhibited filament of ribonucleoside-diphosphate reductase compos...

SupramoleculeName: Inhibited filament of ribonucleoside-diphosphate reductase composed of NrdE alpha subunits and NrdF beta subunit tails
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Beta subunit core density only visible at low threshold. Beta subunit tail is bound with strong density to alpha subunit and modeled as a poly-A peptide in the model.
Source (natural)Organism: Bacillus subtilis (bacteria)

-
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: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 80.791469 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSQNQVPKWI QLNNEIMIQK DGKFQFDKDK EAVHSYFVDY INQNTVFFHN LKEKLDYLVE NQYYEEEFLS LYSFEDIKEV FKTAYAKKF RFPSFMSAFK FYNDYALKTN DKKKILERYE DRISIVALFF ANGDTEKAKE YVNLMINQEY QPSTPTFLNA G RKRRGELV ...String:
MSQNQVPKWI QLNNEIMIQK DGKFQFDKDK EAVHSYFVDY INQNTVFFHN LKEKLDYLVE NQYYEEEFLS LYSFEDIKEV FKTAYAKKF RFPSFMSAFK FYNDYALKTN DKKKILERYE DRISIVALFF ANGDTEKAKE YVNLMINQEY QPSTPTFLNA G RKRRGELV SCFLLEVNDS LNDISRAIDI SMQLSKLGGG VSLNLSKLRA KGEAIKDVEN ATKGVVGVMK LLDNAFRYAD QM GQRQGSG AAYLNIFHRD INDFLDTKKI SADEDVRVKT LSIGVVIPDK FVELAREDKA AYVFYPHTIY KEYGQHMDEM DMN EMYDKF VDNPRVKKEK INPRKLLEKL AMLRSESGYP YIMFQDNVNK VHANNHISKV KFSNLCSEVL QASQVSSYTD YDEE DEIGL DISCNLGSLN ILNVMEHKSI EKTVKLATDS LTHVSETTDI RNAPAVRRAN KAMKSIGLGA MNLHGYLAQN GIAYE SPEA RDFANTFFMM VNFYSIQRSA EIAKEKGETF DQYEGSTYAT GEYFDKYVST DFSPKYEKIA NLFEGMHIPT TEDWKK LKA FVAEHGMYHS YRLCIAPTGS ISYVQSSTAS VMPIMERIEE RTYGNSKTYY PMPGLASNNW FFYKEAYDMD MFKVVDM IA TIQQHIDQGI SFTLFLKDTM TTRDLNRIDL YAHHRGIKTI YYARTKDTGQ DSCLSCVV

UniProtKB: Ribonucleoside-diphosphate reductase

-
Macromolecule #2: Ribonucleoside-diphosphate reductase NrdF beta subunit

MacromoleculeName: Ribonucleoside-diphosphate reductase NrdF beta subunit
type: protein_or_peptide / ID: 2 / Details: C-terminus modeled as a polyalanine chain / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 698.854 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

-
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 / Deoxyadenosine triphosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.40 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chloridesodium chloride
15.0 mMMgCl2magnesium chloride
1.0 mMC9H15O6PTCEP

Details: Glycerol in original storage buffer was diluted to < 0.25% w/v.
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP
DetailsCryo-EM samples of the NrdEF filament were prepared by mixing 20 uM C382S holo-NrdE with 20 or 40 uM Mn-reconstituted NrdF in assay buffer with 100 uM dATP and 1 mM CDP, prior to dilution with nucleotide-containing buffer to a concentration of 5 uM protein. A subset of the grids were pre-coated with a support film of continuous, amorphous carbon by flotation of cleaved mica. For these grids, the sample was diluted to a final protein concentration of 2 uM.

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 130000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number real images: 2843 / Average electron dose: 8.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Segment selectionNumber selected: 281591
Startup modelType of model: OTHER / Details: ab initio model
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 2.0.27)
Final reconstructionApplied symmetry - Helical parameters - Δz: 73.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 88.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.0.27) / Number images used: 126224
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6cgn


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Target criteria: Correlation coefficient
Output model

PDB-6mw3:
EM structure of Bacillus subtilis ribonucleotide reductase inhibited filament composed of NrdE alpha subunit and NrdF beta subunit with dATP

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more