+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21661 | |||||||||
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Title | Hexameric NanR-DNA hetero-complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | NanR dimer-DNA hetero-complex / transcriptional regulator / GntR superfamily / sialic acid / Neu5Ac / cooperativity / Gene regulation. / GENE REGULATION | |||||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.3 Å | |||||||||
Authors | Hariprasad V / Horne C | |||||||||
Funding support | New Zealand, 1 items
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Citation | Journal: Nat Commun / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21661.map.gz | 35.6 MB | EMDB map data format | |
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Header (meta data) | emd-21661-v30.xml emd-21661.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21661_fsc.xml | 9.5 KB | Display | FSC data file |
Images | emd_21661.png | 78.8 KB | ||
Masks | emd_21661_msk_1.map | 70.2 MB | Mask map | |
Filedesc metadata | emd-21661.cif.gz | 6.2 KB | ||
Others | emd_21661_half_map_1.map.gz emd_21661_half_map_2.map.gz | 65.2 MB 65.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21661 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21661 | HTTPS FTP |
-Validation report
Summary document | emd_21661_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_21661_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_21661_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | emd_21661_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21661 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21661 | HTTPS FTP |
-Related structure data
Related structure data | 6wg7MC 6wfqC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21661.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
File | emd_21661_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_21661_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_21661_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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: Escherichia coli (E. coli) |
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: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 29.566354 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
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 | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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. |
-Electron microscopy
Microscope | TFS TALOS |
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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 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: RIGID BODY FIT | ||||||
Output model | PDB-6wg7: |