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Yorodumi- PDB-8dky: Crystal structure of the Aquifex aeolicus Wzt Carbohydrate Bindin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dky | ||||||
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Title | Crystal structure of the Aquifex aeolicus Wzt Carbohydrate Binding Domain bound to 3-O-methyl-D-mannose | ||||||
Components | ABC transporter | ||||||
Keywords | SUGAR BINDING PROTEIN / O antigen ABC transporter / carbohydrate binding domain / 3-O-methyl-D-mannose | ||||||
Function / homology | Function and homology information ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Aquifex aeolicus VF5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Spellmon, N. / Zimmer, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Molecular basis for polysaccharide recognition and modulated ATP hydrolysis by the O antigen ABC transporter. Authors: Nicholas Spellmon / Artur Muszyński / Ireneusz Górniak / Jiri Vlach / David Hahn / Parastoo Azadi / Jochen Zimmer / Abstract: O antigens are ubiquitous protective extensions of lipopolysaccharides in the extracellular leaflet of the Gram-negative outer membrane. Following biosynthesis in the cytosol, the lipid-linked ...O antigens are ubiquitous protective extensions of lipopolysaccharides in the extracellular leaflet of the Gram-negative outer membrane. Following biosynthesis in the cytosol, the lipid-linked polysaccharide is transported to the periplasm by the WzmWzt ABC transporter. Often, O antigen secretion requires the chemical modification of its elongating terminus, which the transporter recognizes via a carbohydrate-binding domain (CBD). Here, using components from A. aeolicus, we identify the O antigen structure with methylated mannose or rhamnose as its cap. Crystal and cryo electron microscopy structures reveal how WzmWzt recognizes this cap between its carbohydrate and nucleotide-binding domains in a nucleotide-free state. ATP binding induces drastic conformational changes of its CBD, terminating interactions with the O antigen. ATPase assays and site directed mutagenesis reveal reduced hydrolytic activity upon O antigen binding, likely to facilitate polymer loading into the ABC transporter. Our results elucidate critical steps in the recognition and translocation of polysaccharides by ABC transporters. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dky.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dky.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 8dky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dky_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8dky_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8dky_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 8dky_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/8dky ftp://data.pdbj.org/pub/pdb/validation_reports/dk/8dky | HTTPS FTP |
-Related structure data
Related structure data | 8dkuC 8dl0C 8dn8C 8dncC 8dneC 8douC 6o14S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16643.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: abcT4, aq_1094 / Production host: Escherichia coli (E. coli) / References: UniProt: O67181 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 20% PEG 3350, 0.1M Tricine pH 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→95.32 Å / Num. obs: 41212 / % possible obs: 99.3 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.037 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.61→1.64 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 2 / Num. unique obs: 1844 / CC1/2: 0.809 / Rpim(I) all: 0.355 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6O14 Resolution: 1.61→48.64 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54 Å2 / Biso mean: 26.3494 Å2 / Biso min: 11.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.61→48.64 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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