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- EMDB-14844: cryo-EM structure of CGT ABC transporter in vanadate trapped state -
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Open data
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Basic information
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Title | cryo-EM structure of CGT ABC transporter in vanadate trapped state | ||||||||||||
![]() | van | ||||||||||||
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![]() | cyclic-beta-glucan / ABC transporter / CGT / Brucella / SUGAR BINDING PROTEIN | ||||||||||||
Function / homology | ![]() ABC-type beta-glucan transporter / ABC-type beta-glucan transporter activity / ATPase-coupled lipid transmembrane transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
![]() | Jaroslaw S / Dong CN / Frank L / Na W / Renato Z / Seunho J / Henning S / Christoph D | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of cyclic β-glucan export by ABC transporter Cgt of Brucella. Authors: Jaroslaw Sedzicki / Dongchun Ni / Frank Lehmann / Na Wu / Renato Zenobi / Seunho Jung / Henning Stahlberg / Christoph Dehio / ![]() ![]() Abstract: Polysaccharides play critical roles in bacteria, including the formation of protective capsules and biofilms and establishing specific host cell interactions. Their transport across membranes is ...Polysaccharides play critical roles in bacteria, including the formation of protective capsules and biofilms and establishing specific host cell interactions. Their transport across membranes is often mediated by ATP-binding cassette (ABC) transporters, which utilize ATP to translocate diverse molecules. Cyclic β-glucans (CβGs) are critical for host interaction of the Rhizobiales, including the zoonotic pathogen Brucella. CβGs are exported into the periplasmic space by the cyclic glucan transporter (Cgt). The interaction of an ABC transporter with a polysaccharide substrate has not been visualized so far. Here we use single-particle cryoelectron microscopy to elucidate the structures of Cgt from Brucella abortus in four conformational states. The substrate-bound structure reveals an unusual binding pocket at the height of the cytoplasmic leaflet, whereas ADP-vanadate models hint at an alternative mechanism of substrate release. Our work provides insights into the translocation of large, heterogeneous substrates and sheds light on protein-polysaccharide interactions in general. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.3 KB 18.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9 KB | Display | ![]() |
Images | ![]() | 64.8 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 49 MB 49 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zo9MC ![]() 7znuC ![]() 7zo8C ![]() 7zoaC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.025 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: van
File | emd_14844_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: van
File | emd_14844_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : CGT ABC transporter vanadate ADP in nanodisc
Entire | Name: CGT ABC transporter vanadate ADP in nanodisc |
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Components |
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-Supramolecule #1: CGT ABC transporter vanadate ADP in nanodisc
Supramolecule | Name: CGT ABC transporter vanadate ADP in nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 125 KDa |
-Macromolecule #1: Beta-(1-->2)glucan export ATP-binding/permease protein NdvA
Macromolecule | Name: Beta-(1-->2)glucan export ATP-binding/permease protein NdvA type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type beta-glucan transporter |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 66.027914 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSLLKIYWRA MQYLAVERTA TITMCVASVL VALVTLAEPV LFGRVIQSIS DKGDIFSPLL MWAALGGFNI MAAVFVARGA DRLAHRRRL GVMIDSYERL ITMPLAWHQK RGTSNALHTL IRATDSLFTL WLEFMRQHLT TVVALATLIP VAMTMDMRMS L VLIVLGVI ...String: MSLLKIYWRA MQYLAVERTA TITMCVASVL VALVTLAEPV LFGRVIQSIS DKGDIFSPLL MWAALGGFNI MAAVFVARGA DRLAHRRRL GVMIDSYERL ITMPLAWHQK RGTSNALHTL IRATDSLFTL WLEFMRQHLT TVVALATLIP VAMTMDMRMS L VLIVLGVI YVMIGQLVMR KTKDGQAAVE KHHHKLFEHV SDTISNVSVV QSYNRIASET QALRDYAKNL ENAQFPVLNW WA LASGLNR MASTFSMVVV LVLGAYFVTK GQMRVGDVIA FIGFAQLMIG RLDQISAFIN QTVTARAKLE EFFQMEDATA DRQ EPENVA DLNDVKGDIV FDNVTYEFPN SGQGVYDVSF EVKPGQTVAI VGPTGAGKTT LINLLQRVFD PAAGRIMIDG TDTR TVSRR SLRHAIATVF QDAGLFNRSV EDNIRVGRAN ATHEEVHAAA KAAAAHDFIL AKSEGYDTFV GERGSQLSGG ERQRL AIAR AILKDSPILV LDEATSALDV ETEEKVTQAV DELSHNRTTF IIAHRLSTVR SADLVLFMDK GHLVESGSFN ELAERG GRF SDLLRAGGLK LEDKQPKQPV VEGSNVMPFP VKGAVA UniProtKB: Beta-(1-->2)glucan export ATP-binding/permease protein NdvA |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #3: VANADATE ION
Macromolecule | Name: VANADATE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: VO4 |
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Molecular weight | Theoretical: 114.939 Da |
Chemical component information | ![]() ChemComp-VN3: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
Details | abc transporter |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 101 |
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Output model | ![]() PDB-7zo9: |