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Open data
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Basic information
Entry | Database: PDB / ID: 7oz3 | |||||||||
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Title | S. agalactiae BusR in complex with its busA-promotor DNA | |||||||||
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![]() | DNA BINDING PROTEIN / Repressor / complex / GntR / Transcription | |||||||||
Function / homology | ![]() monoatomic cation transmembrane transporter activity / potassium ion transport / DNA-binding transcription factor activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.46 Å | |||||||||
![]() | Bandera, A.M. / Witte, G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture. Authors: Adrian M Bandera / Joseph Bartho / Katja Lammens / David Jan Drexler / Jasmin Kleinschwärzer / Karl-Peter Hopfner / Gregor Witte / ![]() Abstract: The cyclic dinucleotide second messenger c-di-AMP is a major player in regulation of potassium homeostasis and osmolyte transport in a variety of bacteria. Along with various direct interactions with ...The cyclic dinucleotide second messenger c-di-AMP is a major player in regulation of potassium homeostasis and osmolyte transport in a variety of bacteria. Along with various direct interactions with proteins such as potassium channels, the second messenger also specifically binds to transcription factors, thereby altering the processes in the cell on the transcriptional level. We here describe the structural and biochemical characterization of BusR from the human pathogen Streptococcus agalactiae. BusR is a member of a yet structurally uncharacterized subfamily of the GntR family of transcription factors that downregulates transcription of the genes for the BusA (OpuA) glycine-betaine transporter upon c-di-AMP binding. We report crystal structures of full-length BusR, its apo and c-di-AMP bound effector domain, as well as cryo-EM structures of BusR bound to its operator DNA. Our structural data, supported by biochemical and biophysical data, reveal that BusR utilizes a unique domain assembly with a tetrameric coiled-coil in between the binding platforms, serving as a molecular ruler to specifically recognize a 22 bp separated bipartite binding motif. Binding of c-di-AMP to BusR induces a shift in equilibrium from an inactivated towards an activated state that allows BusR to bind the target DNA, leading to transcriptional repression. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.9 KB | Display | ![]() |
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PDB format | ![]() | 152.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 929.4 KB | Display | ![]() |
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Full document | ![]() | 942.1 KB | Display | |
Data in XML | ![]() | 37.7 KB | Display | |
Data in CIF | ![]() | 52.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 13119MC ![]() 7b5tC ![]() 7b5uC ![]() 7b5wC ![]() 7b5yC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 23880.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BM110_ORF1201, AX245_01365, C6N10_09995, F5043_05515, GD434_05225, RDF_1124 Production host: ![]() ![]() #2: DNA chain | | Mass: 46903.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #3: DNA chain | | Mass: 46903.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: transcriptional repressor BusR bound to target DNA / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | |||||||||||||||
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Molecular weight | Value: 0.122 MDa | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Buffer solution | pH: 6.5 / Details: degassed, filtered | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K Details: 0.05% beta-octyl glycoside added prior to plunge freezing |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112451 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 177 / Protocol: FLEXIBLE FIT / Space: REAL Details: RCK_C domains were build by rigid body fit of the model 7B5U. The flexible linker between RCK_C domain and coiled-coil domain were build de novo. | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 134.6 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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