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- EMDB-14801: Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its... -
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Open data
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Basic information
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Title | Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the closed conformation, C2 symmetry | |||||||||
![]() | Full cryo-EM map of holo-PdxR in complex with its target dsDNA in the closed conformation (C2 symmetry) | |||||||||
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![]() | transcription factor / PLP-binding protein / domain-swap homodimer / DNA binding protein | |||||||||
Function / homology | ![]() transaminase activity / biosynthetic process / pyridoxal phosphate binding / DNA-binding transcription factor activity / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Freda I / Montemiglio LC / Tramonti A / Contestabile R / Vallone B / Exertier C / Savino C / Chaves Sanjuan A / Bolognesi M | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR. Authors: Ida Freda / Cécile Exertier / Anna Barile / Antonio Chaves-Sanjuan / Mirella Vivoli Vega / Michail N Isupov / Nicholas J Harmer / Elena Gugole / Paolo Swuec / Martino Bolognesi / Anita ...Authors: Ida Freda / Cécile Exertier / Anna Barile / Antonio Chaves-Sanjuan / Mirella Vivoli Vega / Michail N Isupov / Nicholas J Harmer / Elena Gugole / Paolo Swuec / Martino Bolognesi / Anita Scipioni / Carmelinda Savino / Martino Luigi Di Salvo / Roberto Contestabile / Beatrice Vallone / Angela Tramonti / Linda Celeste Montemiglio / ![]() ![]() Abstract: Specificity in protein-DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered ...Specificity in protein-DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered the nature of the interactions driving DNA recognition and binding by the bacterial transcription factor PdxR, a member of the MocR family responsible for the regulation of pyridoxal 5'-phosphate (PLP) biosynthesis. Single particle cryo-EM performed on the PLP-PdxR bound to its target DNA enabled the isolation of three conformers of the complex, which may be considered as snapshots of the binding process. Moreover, the resolution of an apo-PdxR crystallographic structure provided a detailed description of the transition of the effector domain to the holo-PdxR form triggered by the binding of the PLP effector molecule. Binding analyses of mutated DNA sequences using both wild type and PdxR variants revealed a central role of electrostatic interactions and of the intrinsic asymmetric bending of the DNA in allosterically guiding the holo-PdxR-DNA recognition process, from the first encounter through the fully bound state. Our results detail the structure and dynamics of the PdxR-DNA complex, clarifying the mechanism governing the DNA-binding mode of the holo-PdxR and the regulation features of the MocR family of transcription factors. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 58.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.2 KB 21.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 45.8 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() | 48.5 MB 48.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 855.9 KB | Display | ![]() |
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Full document | ![]() | 855.5 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zn5MC ![]() 7pq9C ![]() 7zlaC ![]() 7zpaC ![]() 7zthC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Full cryo-EM map of holo-PdxR in complex with its target dsDNA in the closed conformation (C2 symmetry) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.889 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half cryo-EM map 2 of holo-PdxR in complex...
File | emd_14801_half_map_1.map | ||||||||||||
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Annotation | Half cryo-EM map 2 of holo-PdxR in complex with its target dsDNA in the closed conformation (C2 symmetry) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half cryo-EM map 1 of holo-PdxR in complex...
File | emd_14801_half_map_2.map | ||||||||||||
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Annotation | Half cryo-EM map 1 of holo-PdxR in complex with its target dsDNA in the closed conformation (C2 symmetry) | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Binary complex between the PLP-bound homodimeric PdxR and a 48bp ...
Entire | Name: Binary complex between the PLP-bound homodimeric PdxR and a 48bp double strand DNA fragment |
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Components |
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-Supramolecule #1: Binary complex between the PLP-bound homodimeric PdxR and a 48bp ...
Supramolecule | Name: Binary complex between the PLP-bound homodimeric PdxR and a 48bp double strand DNA fragment type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 136 KDa |
-Macromolecule #1: PLP-dependent aminotransferase family protein
Macromolecule | Name: PLP-dependent aminotransferase family protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 55.499121 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MELLWCELNR DLPTPLYEQL YAHIKTEITE GRIGYGTKLP SKRKLADSLK LSQNTVEAAY EQLVAEGYVE VIPRKGFYVQ AYEDLEYIR APQAPGDALA TKQDTIRYNF HPTHIDTTSF PFEQWRKYFK QTMCKENHRL LLNGDHQGEA SFRREIAYYL H HSRGVNCT ...String: MELLWCELNR DLPTPLYEQL YAHIKTEITE GRIGYGTKLP SKRKLADSLK LSQNTVEAAY EQLVAEGYVE VIPRKGFYVQ AYEDLEYIR APQAPGDALA TKQDTIRYNF HPTHIDTTSF PFEQWRKYFK QTMCKENHRL LLNGDHQGEA SFRREIAYYL H HSRGVNCT PEQVVVGAGV ETLLQQLFLL LGESKVYGIE DPGYQLMRKL LSHYPNDYVP FQVDEEGIDV DSIVRTAVDV VY TTPSRHF PYGSVLSINR RKQLLHWAEA HENRYIIEDD YDSEFRYTGK TIPSLQSMDV HNKVIYLGAF S(LLP)SLIPSVR ISYMVLPAPL AHLYKNKFSY YHSTVSRIDQ QVLTAFMKQG DFEKHLNRMR KIYRRKLEKV LSLLKRYEDK LLIIGERSGL HIVLVVKNG MDEQTLVEKA LAAKAKVYPL SAYSLERAIH PPQIVLGFGS IPEDELEEAI ATVLNAWGFL VPRGSLEHHH H HH UniProtKB: PLP-dependent aminotransferase family protein |
-Macromolecule #2: DNA (48-MER)
Macromolecule | Name: DNA (48-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.667447 KDa |
Sequence | String: (DC)(DT)(DG)(DA)(DC)(DC)(DT)(DC)(DA)(DT) (DC)(DA)(DT)(DT)(DT)(DT)(DC)(DT)(DT)(DA) (DA)(DA)(DA)(DA)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DT)(DT)(DA)(DC)(DA)(DA)(DT)(DG) (DT) (DG)(DG)(DT)(DC)(DA)(DG)(DT)(DT) |
-Macromolecule #3: DNA (48-MER)
Macromolecule | Name: DNA (48-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.894607 KDa |
Sequence | String: (DA)(DA)(DC)(DT)(DG)(DA)(DC)(DC)(DA)(DC) (DA)(DT)(DT)(DG)(DT)(DA)(DA)(DG)(DT)(DG) (DT)(DC)(DA)(DG)(DT)(DT)(DT)(DT)(DT) (DA)(DA)(DG)(DA)(DA)(DA)(DA)(DT)(DG)(DA) (DT) (DG)(DA)(DG)(DG)(DT)(DC)(DA)(DG) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL | ||||||
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Buffer | pH: 7.5 / Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: GloQube system (Quorum Technologies) | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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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: 3284 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 142 | ||||||
Output model | ![]() PDB-7zn5: |