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Yorodumi- EMDB-14845: cryo-EM structure of CGT ABC transporter in presence of CBG substrate -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14845 | ||||||||||||
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Title | cryo-EM structure of CGT ABC transporter in presence of CBG substrate | ||||||||||||
Map data | sugar | ||||||||||||
Sample |
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Keywords | cyclic-beta-glucan / ABC transporter / CGT / Brucella / SUGAR BINDING PROTEIN | ||||||||||||
Function / homology | Function and homology information ABC-type beta-glucan transporter / ABC-type beta-glucan transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Brucella abortus 2308 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||
Authors | Jaroslaw S / Dong CN / Frank L / Na W / Renato Z / Seunho J / Henning S / Christoph D | ||||||||||||
Funding support | Switzerland, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 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 | emd_14845.map.gz | 49.7 MB | EMDB map data format | |
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Header (meta data) | emd-14845-v30.xml emd-14845.xml | 24.4 KB 24.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14845_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_14845.png | 70.9 KB | ||
Filedesc metadata | emd-14845.cif.gz | 6.3 KB | ||
Others | emd_14845_additional_1.map.gz emd_14845_additional_2.map.gz emd_14845_additional_3.map.gz emd_14845_half_map_1.map.gz emd_14845_half_map_2.map.gz | 49.7 MB 49.7 MB 49.6 MB 49 MB 49 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14845 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14845 | HTTPS FTP |
-Validation report
Summary document | emd_14845_validation.pdf.gz | 822.7 KB | Display | EMDB validaton report |
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Full document | emd_14845_full_validation.pdf.gz | 822.3 KB | Display | |
Data in XML | emd_14845_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | emd_14845_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14845 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14845 | HTTPS FTP |
-Related structure data
Related structure data | 7zoaMC 7znuC 7zo8C 7zo9C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14845.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | sugar | ||||||||||||||||||||||||||||||||||||
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
-Additional map: sugar
File | emd_14845_additional_1.map | ||||||||||||
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Annotation | sugar | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: sugar
File | emd_14845_additional_2.map | ||||||||||||
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Annotation | sugar | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: sugar
File | emd_14845_additional_3.map | ||||||||||||
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Annotation | sugar | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: sugar
File | emd_14845_half_map_1.map | ||||||||||||
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Annotation | sugar | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: sugar
File | emd_14845_half_map_2.map | ||||||||||||
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Annotation | sugar | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of CGT ABC transporter with the substrate Cyclic beta glucan
Entire | Name: Complex of CGT ABC transporter with the substrate Cyclic beta glucan |
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Components |
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-Supramolecule #1: Complex of CGT ABC transporter with the substrate Cyclic beta glucan
Supramolecule | Name: Complex of CGT ABC transporter with the substrate Cyclic beta glucan type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Brucella abortus 2308 (bacteria) |
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: Brucella abortus 2308 (bacteria) / Strain: 2308 |
Molecular weight | Theoretical: 66.027914 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
Details | abc transporter CBG complex |
-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: FIELD EMISSION GUN |
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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 180 |
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Output model | PDB-7zoa: |