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- EMDB-50849: Cryo-EM structure of E. coli transcription factor NrdR in the ATP... -

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Basic information

Entry
Database: EMDB / ID: EMD-50849
TitleCryo-EM structure of E. coli transcription factor NrdR in the ATP-bound, filamentous form
Map dataSharpened map from cryoSPARC
Sample
  • Organelle or cellular component: E. coli NrdR
    • Protein or peptide: E. coli NrdR
Keywordstranscription factor / ribonucleotide reductase / repressor / ATP-cone / Zn-ribbon / DNA BINDING PROTEIN
Function / homology
Function and homology information


double-stranded DNA binding / negative regulation of DNA-templated transcription / zinc ion binding / ATP binding
Similarity search - Function
Ribonucleotide reductase regulator NrdR-like / : / Transcriptional repressor NrdR-like, N-terminal domain / ATP-cone domain / ATP cone domain / ATP-cone domain profile.
Similarity search - Domain/homology
Transcriptional repressor NrdR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsMartinez-Carranza M / Rozman Grinberg I / Sjoberg BM / Logan DT / Stenmark P
Funding support Sweden, United States, 6 items
OrganizationGrant numberCountry
Carl Trygger FoundationCTS 20:361 Sweden
Cancerfonden201210PJF Sweden
Wenner-Gren Foundation United States
Swedish Research Council2016-04855 Sweden
Swedish Research Council2019-03681 Sweden
Swedish Research Council2023-05074 Sweden
CitationJournal: FEBS J / Year: 2025
Title: Bacterial transcriptional repressor NrdR - a flexible multifactorial nucleotide sensor.
Authors: Inna Rozman Grinberg / Ornella Bimaï / Saher Shahid / Lena Philipp / Markel Martínez-Carranza / Ipsita Banerjee / Daniel Lundin / Pål Stenmark / Britt-Marie Sjöberg / Derek T Logan /
Abstract: NrdR is a bacterial transcriptional repressor consisting of a zinc (Zn)-ribbon domain followed by an ATP-cone domain. Understanding its mechanism of action could aid the design of novel ...NrdR is a bacterial transcriptional repressor consisting of a zinc (Zn)-ribbon domain followed by an ATP-cone domain. Understanding its mechanism of action could aid the design of novel antibacterials. NrdR binds specifically to two "NrdR boxes" upstream of ribonucleotide reductase operons, of which Escherichia coli has three: nrdHIEF, nrdDG and nrdAB, in the last of which we identified a new box. We show that E. coli NrdR (EcoNrdR) has similar binding strength to all three sites when loaded with ATP plus deoxyadenosine triphosphate (dATP) or equivalent diphosphate combinations. No other combination of adenine nucleotides promotes binding to DNA. We present crystal structures of EcoNrdR-ATP-dATP and EcoNrdR-ADP-dATP, which are the first high-resolution crystal structures of an NrdR. We have also determined cryo-electron microscopy structures of DNA-bound EcoNrdR-ATP-dATP and novel filaments of EcoNrdR-ATP. Tetrameric forms of EcoNrdR involve alternating interactions between pairs of Zn-ribbon domains and ATP-cones. The structures reveal considerable flexibility in relative orientation of ATP-cones vs Zn-ribbon domains. The structure of DNA-bound EcoNrdR-ATP-dATP shows that significant conformational rearrangements between ATP-cones and Zn-ribbons accompany DNA binding while the ATP-cones retain the same relative orientation. In contrast, ATP-loaded EcoNrdR filaments show rearrangements of the ATP-cone pairs and sequester the DNA-binding residues of NrdR such that they are unable to bind to DNA. Our results, in combination with a previous structural and biochemical study, point to highly flexible EcoNrdR structures that, when loaded with the correct nucleotides, adapt to an optimal promoter-binding conformation.
History
DepositionJul 1, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50849.png

Downloads & links

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Map

FileDownload / File: emd_50849.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from cryoSPARC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 338.56 Å		0.85 Å/pix.
x 400 pix.
= 338.56 Å		0.85 Å/pix.
x 400 pix.
= 338.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.2751358 - 2.967398
Average (Standard dev.)0.0016425562 (±0.050186936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 338.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50849_msk_1.map
Projections & Slices
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Additional map: Unsharpened map from cryoSPARC

Fileemd_50849_additional_1.map
AnnotationUnsharpened map from cryoSPARC
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_50849_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_50849_half_map_2.map
Projections & Slices
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Sample components

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Entire : E. coli NrdR

EntireName: E. coli NrdR
Components
  • Organelle or cellular component: E. coli NrdR
    • Protein or peptide: E. coli NrdR

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Supramolecule #1: E. coli NrdR

SupramoleculeName: E. coli NrdR / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Transcription factor NrdR from E. coli in complex with ATP
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: E. coli NrdR

MacromoleculeName: E. coli NrdR / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHCPFCFAVD TKVIDSRLVG EGSSVRRRRQ CLVCNERFTT FEVAELVMPR VVKSNDVREP FNEEKLRSGM LRALEKRPV SSDDVEMAIN HIKSQLRATG EREVPSKMIG NLVMEQLKKL DKVAYIRFAS VYRSFEDIKD F GEEIARLE DKLAAALEHH HHHH

UniProtKB: Transcriptional repressor NrdR

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 9
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
5.0 mMDTTdithiothreitol
0.2 mMMgCl2magnesium chloride
0.1 mMATPadenosine triphosphate
50.0 mMTris-HClTris-HCl buffer
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.0 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: 3.0 µm / Nominal defocus min: 1.6 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

CTF correctionSoftware - Name: cryoSPARC (ver. 2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.1) / Number images used: 133931
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.1)
Final 3D classificationNumber classes: 2 / Avg.num./class: 87377 / Software - Name: cryoSPARC (ver. 2.1)
Details: Class 1: 133,931 particles Class 2: 40,774 particles
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: unpublished ATP-dATP complex
DetailsTetramers of the dATP-ATP-bound form of E. coli NrdR were fitted to the map of the ATP-bound form domain-wise. ATP-cone pairs were allowed to move relative to each other while Zn-ribbon pairs were kept in fixed relative orientation.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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