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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21661 | |||||||||
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Title | Hexameric NanR-DNA hetero-complex | |||||||||
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![]() | NanR dimer-DNA hetero-complex / ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Hariprasad V / Horne C | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism. Authors: Christopher R Horne / Hariprasad Venugopal / Santosh Panjikar / David M Wood / Amy Henrickson / Emre Brookes / Rachel A North / James M Murphy / Rosmarie Friemann / Michael D W Griffin / ...Authors: Christopher R Horne / Hariprasad Venugopal / Santosh Panjikar / David M Wood / Amy Henrickson / Emre Brookes / Rachel A North / James M Murphy / Rosmarie Friemann / Michael D W Griffin / Georg Ramm / Borries Demeler / Renwick C J Dobson / ![]() ![]() ![]() ![]() ![]() Abstract: Bacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and ...Bacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 35.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.4 KB 18.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.5 KB | Display | ![]() |
Images | ![]() | 78.8 KB | ||
Masks | ![]() | 70.2 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 65.2 MB 65.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wg7MC ![]() 6wfqC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.94 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #1
File | emd_21661_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_21661_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Hexameric NanR-DNA hetero-complex
Entire | Name: Hexameric NanR-DNA hetero-complex |
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Components |
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-Supramolecule #1: Hexameric NanR-DNA hetero-complex
Supramolecule | Name: Hexameric NanR-DNA hetero-complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Hexameric NanR-DNA hetero-complex |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 198.5 KDa |
-Macromolecule #1: DNA (35-MER)
Macromolecule | Name: DNA (35-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 10.856016 KDa |
Sequence | String: (DT)(DT)(DG)(DA)(DT)(DC)(DT)(DG)(DG)(DT) (DA)(DT)(DA)(DA)(DC)(DA)(DG)(DG)(DT)(DA) (DT)(DA)(DA)(DA)(DG)(DG)(DT)(DA)(DT) (DA)(DT)(DC)(DG)(DT)(DT) |
-Macromolecule #2: DNA (35-MER)
Macromolecule | Name: DNA (35-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 10.673923 KDa |
Sequence | String: (DA)(DA)(DC)(DG)(DA)(DT)(DA)(DT)(DA)(DC) (DC)(DT)(DT)(DT)(DA)(DT)(DA)(DC)(DC)(DT) (DG)(DT)(DT)(DA)(DT)(DA)(DC)(DC)(DA) (DG)(DA)(DT)(DC)(DA)(DA) |
-Macromolecule #3: HTH-type transcriptional repressor NanR
Macromolecule | Name: HTH-type transcriptional repressor NanR / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 29.566354 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MGLMNAFDSQ TEDSSPAIGR NLRSRPLARK KLSEMVEEEL EQMIRRREFG EGEQLPSERE LMAFFNVGRP SVREALAALK RKGLVQINN GERARVSRPS ADTIIGELSG MAKDFLSHPG GIAHFEQLRL FFESSLVRYA AEHATDEQID LLAKALEINS Q SLDNNAAF ...String: MGLMNAFDSQ TEDSSPAIGR NLRSRPLARK KLSEMVEEEL EQMIRRREFG EGEQLPSERE LMAFFNVGRP SVREALAALK RKGLVQINN GERARVSRPS ADTIIGELSG MAKDFLSHPG GIAHFEQLRL FFESSLVRYA AEHATDEQID LLAKALEINS Q SLDNNAAF IRSDVDFHRV LAEIPGNPIF MAIHVALLDW LIAARPTVTD QALHEHNNVS YQQHIAIVDA IRRHDPDEAD RA LQSHLNS VSATWHAFGQ TTNKKK UniProtKB: HTH-type transcriptional repressor NanR |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 / Details: 20mM Tris-HCL,50mM NaCl, pH 8.0 |
Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III / Details: Blot force: -3 Blot time: 3 sec Drain time: 0. |
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Electron microscopy
Microscope | TFS TALOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2287 / Average exposure time: 51.54 sec. / Average electron dose: 45.0 e/Å2 |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: RIGID BODY FIT | ||||||
Output model | ![]() PDB-6wg7: |